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Slieker RC, Warmerdam DO, Vermeer MH, van Doorn R, Heemskerk MHM, Scheeren FA. Reassessing human MHC-I genetic diversity in T cell studies. Sci Rep 2024; 14:7966. [PMID: 38575727 PMCID: PMC10995142 DOI: 10.1038/s41598-024-58777-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 04/03/2024] [Indexed: 04/06/2024] Open
Abstract
The Major Histocompatibility Complex class I (MHC-I) system plays a vital role in immune responses by presenting antigens to T cells. Allele specific technologies, including recombinant MHC-I technologies, have been extensively used in T cell analyses for COVID-19 patients and are currently used in the development of immunotherapies for cancer. However, the immense diversity of MHC-I alleles presents challenges. The genetic diversity serves as the foundation of personalized medicine, yet it also poses a potential risk of exacerbating healthcare disparities based on MHC-I alleles. To assess potential biases, we analysed (pre)clinical publications focusing on COVID-19 studies and T cell receptor (TCR)-based clinical trials. Our findings reveal an underrepresentation of MHC-I alleles associated with Asian, Australian, and African descent. Ensuring diverse representation is vital for advancing personalized medicine and global healthcare equity, transcending genetic diversity. Addressing this disparity is essential to unlock the full potential of T cells for enhancing diagnosis and treatment across all individuals.
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Affiliation(s)
- Roderick C Slieker
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
- Leiden Center for Computational Oncology, Leiden University Medical Center, Leiden, The Netherlands
| | - Daniël O Warmerdam
- Centre for Future Affordable & Sustainable Therapy Development (FAST), The Hague, The Netherlands
| | - Maarten H Vermeer
- Department of Dermatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Remco van Doorn
- Department of Dermatology, Leiden University Medical Center, Leiden, The Netherlands
- Department of Dermatology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Mirjam H M Heemskerk
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - Ferenc A Scheeren
- Department of Dermatology, Leiden University Medical Center, Leiden, The Netherlands.
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2
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Yang KL, Lin PY. Association of HLA-C*07:359 with HLA-A, -B, and -DRB1 alleles in Taiwanese. Tzu Chi Med J 2024; 36:166-174. [PMID: 38645783 PMCID: PMC11025586 DOI: 10.4103/tcmj.tcmj_288_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 12/03/2023] [Accepted: 12/26/2023] [Indexed: 04/23/2024] Open
Abstract
Objectives It is thought that Taiwanese indigenous people were the "first people" to populate Taiwan (Formosa) having been there for over 5000 years, preceding the Dutch colonization (from 1624 to 1662) and Spanish colonization (from 1626 to 1642). Taiwan's indigenes, represented by Austronesian language speakers, currently constitute approximately 2% of the total population in Taiwan. It is unknown whether they evolved from Taiwan's Paleolithic or Neolithic cultures, arrived during or after the Neolithic period from China or Southeast Asia or both. HLA studies on the Taiwanese indigenous population have found several intriguing genetic information showing one or two relatively frequently observed alleles and a small number of relatively less frequently observed ones. We report here a relatively frequently observed HLA-C*07:359 allele in the Taiwanese indigenous population, its linkage with HLA-B*39:01, and its probable associated HLA haplotype in two Taiwanese indigenous families. HLA-C*07:359 is a rarely observed allele in the HLA-C locus in the world populations. The objective of this study is to report the allele HLA-C*07:359 that is more frequently found in the Taiwanese population, especially in the Taiwanese indigenous people, to demonstrate that it has a close linkage with HLA-B*39:01 allele in the HLA-B locus and to show the plausible deduced HLA-A-C-B-DRB1-DQB1 haplotypes in association with HLA-C*07:359 in two families of Taiwanese indigenous unrelated individuals. Materials and Methods The samples were peripheral whole blood, with dipotassium ethylenediaminetetraacetic acid and/or acid citrate dextrose anticoagulation additives. The sequence-based typing method was employed to confirm the low incidence of the allele of HLA-C*07:359 observed in Taiwanese. Polymerase chain reaction was carried out to amplify exons 2, 3, and 4 of the HLA-A,-B,-C,-DRB1 and-DQB1 loci with group-specific primer sets. Amplicons were sequenced using the BigDye Terminator Cycle Sequencing Ready Reaction Kit in both directions according to the manufacturer's protocol. Results C*07:359 is an uncommon allele in the HLA-C locus in the world general population, according to our literature review. However, in this study, it is observed in the general Taiwanese population (frequency 0.41%), especially in the Taiwanese indigenous people at a frequency of 0.23%. In addition, we deduced two probable HLA haplotypes in association with C*07:359 in two indigenous families: A*24:02-C*07:359-B*39:01-DRB1*04:36 and A*24:02-C*07:359-B*39:01-DRB1*04:04. Conclusion The two deduced HLA haplotypes associated with the uncommon C*07:359 allele that we report here are valuable for HLA tissue typing laboratories for reference purposes and for stem cell transplantation donor search coordinators to determine the likelihood of finding compatible donors in unrelated bone marrow donor registries for patients bearing the uncommon HLA allele. Since C*07:359 was found mostly in the Taiwanese indigenous population, we think the allele and its haplotypes we report here are important in population and anthropological studies.
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Affiliation(s)
- Kuo-Liang Yang
- Laboratory of Immunogenetics, Tzu Chi Cord Blood Bank, and Buddhist Tzu Chi Bone Marrow Donor Registry, Buddhist Tzu Chi Stem Cells Centre, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Hualien, Taiwan
- Department of Laboratory Medicine and Biotechnology, Tzu Chi University, Hualien, Taiwan
| | - Py-Yu Lin
- Laboratory of Immunogenetics, Tzu Chi Cord Blood Bank, and Buddhist Tzu Chi Bone Marrow Donor Registry, Buddhist Tzu Chi Stem Cells Centre, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Hualien, Taiwan
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Aguiar Santiago JA, Marrero Miragaya MA, Figueroa Oliva DA, Aguilar Juanes A, Idavoy Corona A, Martínez Fernández S, Morán Bertot I, Rodríguez Hernández M, Canales López E, Hernández Esteves I, Silva Girado JA, Estrada Vázquez RC, Gell Cuesta O, Mendoza-Marí Y, Valdés Prado I, Rodríguez Ibarra C, Palenzuela Gardon DO, Pentón Arias E, Guillén Nieto G, Aguilar Rubido JC. Preparing for the Next Pandemic: Increased Expression of Interferon-Stimulated Genes After Local Administration of Nasalferon or HeberNasvac. DNA Cell Biol 2024; 43:95-102. [PMID: 38118108 DOI: 10.1089/dna.2023.0283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2023] Open
Abstract
HeberNasvac, a therapeutic vaccine for chronic hepatitis B, is able to safely stimulate multiple Toll-like receptors, increasing antigen presentation in vitro and in a phase II clinical trial (Profira) in elderly volunteers who were household contacts of respiratory infection patients. Thus, a new indication as a postexposure prophylaxis or early therapy for respiratory infections has been proposed. In this study, we evaluated the expression of several interferon-stimulated genes (ISGs) after mucosal administration of HeberNasvac and compared this effect with the nasal delivery of interferon alpha 2b (Nasalferon). Molecular studies of blood samples of 50 subjects from the Profira clinical trial who were locally treated with HeberNasvac or Nasalferon and concurrent untreated individuals were compared based on their relative mRNA expression of OAS1, ISG15, ISG20, STAT1, STAT3, and DRB1-HLA II genes. In most cases, the gene expression induced by HeberNasvac was similar in profile and intensity to the expression induced by Nasalferon and significantly superior to that observed in untreated controls. The immune stimulatory effect of HeberNasvac on ISGs paved the way for its future use as an innate immunity stimulator in elderly persons and immunocompromised subjects or as part of Mambisa, a nasal vaccine to prevent severe acute respiratory syndrome coronavirus 2 infection.
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Affiliation(s)
| | | | | | | | | | | | - Ivis Morán Bertot
- Plant Molecular Biology Department, Center for Genetic Engineering and Biotechnology (CIGB), Havana, Cuba
| | | | - Eduardo Canales López
- Plant Genomic Department, Center for Genetic Engineering and Biotechnology (CIGB), Havana, Cuba
| | | | - José Angel Silva Girado
- Olinonucleotide Synthesis Department, Center for Genetic Engineering and Biotechnology (CIGB), Havana, Cuba
| | | | - Omar Gell Cuesta
- Olinonucleotide Synthesis Department, Center for Genetic Engineering and Biotechnology (CIGB), Havana, Cuba
| | - Yssel Mendoza-Marí
- Vaccine Department, Center for Genetic Engineering and Biotechnology (CIGB), Havana, Cuba
| | - Iris Valdés Prado
- Vaccine Department, Center for Genetic Engineering and Biotechnology (CIGB), Havana, Cuba
| | | | | | - Eduardo Pentón Arias
- Vaccine Department, Center for Genetic Engineering and Biotechnology (CIGB), Havana, Cuba
| | - Gerardo Guillén Nieto
- Vaccine Department, Center for Genetic Engineering and Biotechnology (CIGB), Havana, Cuba
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4
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Vică ML, Dobreanu M, Curocichin G, Matei HV, Bâlici Ș, Vușcan ME, Chiorean AD, Nicula GZ, Pavel Mironescu DC, Leucuța DC, Teodoru CA, Siserman CV. The Influence of HLA Polymorphisms on the Severity of COVID-19 in the Romanian Population. Int J Mol Sci 2024; 25:1326. [PMID: 38279325 PMCID: PMC10816224 DOI: 10.3390/ijms25021326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 01/16/2024] [Accepted: 01/20/2024] [Indexed: 01/28/2024] Open
Abstract
In this study, we aimed to investigate whether specific HLA alleles found in patients from Romania and the Republic of Moldova were associated with the severity of COVID-19 infection and its associated mortality. We analyzed the HLA alleles at the -A, -B, -C, -DRB1, and -DQB1 loci in a cohort of 130 individuals with severe and extremely severe forms of COVID-19, including 44 individuals who died. We compared these findings to a control group consisting of individuals who had either not been diagnosed with COVID-19 or had experienced mild forms of the disease. Using multivariate logistic regression models, we discovered that the B*27 and B*50 alleles were associated with an increased susceptibility to developing a severe form of COVID-19. The A*33 and C*15 alleles showed potential for offering protection against the disease. Furthermore, we identified two protective alleles (A*03 and DQB1*02) against the development of extremely severe forms of COVID-19. By utilizing score statistics, we established a statistically significant association between haplotypes and disease severity (p = 0.021). In summary, this study provides evidence that HLA genotype plays a role in influencing the clinical outcome of COVID-19 infection.
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Affiliation(s)
- Mihaela Laura Vică
- Department of Cell and Molecular Biology, “Iuliu Hațieganu” University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania; (M.L.V.); (Ș.B.); (M.E.V.); (A.D.C.); (G.Z.N.); (D.C.P.M.)
- Legal Medicine Institute, 400006 Cluj-Napoca, Romania;
| | - Minodora Dobreanu
- Emergency Clinical County Hospital, 540136 Târgu Mureș, Romania;
- Department of Laboratory Medicine, “George Emil Palade” University of Medicine, Pharmacy, Science and Technology, 540142 Târgu Mureș, Romania
- Center for Advanced Medical and Pharmaceutical Research, “George Emil Palade” University of Medicine, Pharmacy, Science and Technology, 540142 Târgu Mureș, Romania
| | - Ghenadie Curocichin
- Department of Family Medicine, “Nicolae Testemițanu” State University of Medicine and Pharmacy, MD-2004 Chișinău, Moldova;
| | - Horea Vladi Matei
- Department of Cell and Molecular Biology, “Iuliu Hațieganu” University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania; (M.L.V.); (Ș.B.); (M.E.V.); (A.D.C.); (G.Z.N.); (D.C.P.M.)
- Legal Medicine Institute, 400006 Cluj-Napoca, Romania;
| | - Ștefana Bâlici
- Department of Cell and Molecular Biology, “Iuliu Hațieganu” University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania; (M.L.V.); (Ș.B.); (M.E.V.); (A.D.C.); (G.Z.N.); (D.C.P.M.)
| | - Mihaela Elvira Vușcan
- Department of Cell and Molecular Biology, “Iuliu Hațieganu” University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania; (M.L.V.); (Ș.B.); (M.E.V.); (A.D.C.); (G.Z.N.); (D.C.P.M.)
- Legal Medicine Institute, 400006 Cluj-Napoca, Romania;
| | - Alin Dan Chiorean
- Department of Cell and Molecular Biology, “Iuliu Hațieganu” University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania; (M.L.V.); (Ș.B.); (M.E.V.); (A.D.C.); (G.Z.N.); (D.C.P.M.)
- Emergency Clinical Hospital for Children, 400370 Cluj-Napoca, Romania
| | - Gheorghe Zsolt Nicula
- Department of Cell and Molecular Biology, “Iuliu Hațieganu” University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania; (M.L.V.); (Ș.B.); (M.E.V.); (A.D.C.); (G.Z.N.); (D.C.P.M.)
| | - Daniela Cristina Pavel Mironescu
- Department of Cell and Molecular Biology, “Iuliu Hațieganu” University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania; (M.L.V.); (Ș.B.); (M.E.V.); (A.D.C.); (G.Z.N.); (D.C.P.M.)
- Legal Medicine Institute, 400006 Cluj-Napoca, Romania;
| | - Daniel Corneliu Leucuța
- Department of Medical Informatics and Biostatistics, “Iuliu Hațieganu” University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania;
| | - Cosmin Adrian Teodoru
- Clinical Surgical Department, Faculty of Medicine, “Lucian Blaga” University of Sibiu, 550169 Sibiu, Romania;
| | - Costel Vasile Siserman
- Legal Medicine Institute, 400006 Cluj-Napoca, Romania;
- Department of Legal Medicine, “Iuliu Hațieganu” University of Medicine and Pharmacy, 400006 Cluj-Napoca, Romania
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5
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Ferreras C, Hernández-Blanco C, Martín-Quirós A, Al-Akioui-Sanz K, Mora-Rillo M, Ibáñez F, Díaz-Almirón M, Cano-Ochando J, Lozano-Ojalvo D, Jiménez-González M, Goterris R, Sánchez-Zapardiel E, de Paz R, Guerra-García P, Queiruga-Parada J, Molina P, Briones ML, Ruz-Caracuel B, Borobia AM, Carcas AJ, Planelles D, Vicario JL, Moreno MÁ, Balas A, Llano M, Llorente A, Del Balzo Á, Cañada C, García MÁ, Calvin ME, Arenas I, Pérez de Diego R, Eguizábal C, Soria B, Solano C, Pérez-Martínez A. Results of phase 2 randomized multi-center study to evaluate the safety and efficacy of infusion of memory T cells as adoptive therapy in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pneumonia and/or lymphopenia (RELEASE NCT04578210). Cytotherapy 2024; 26:25-35. [PMID: 37897472 DOI: 10.1016/j.jcyt.2023.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 09/05/2023] [Accepted: 10/05/2023] [Indexed: 10/30/2023]
Abstract
BACKGROUND AIMS There are currently no effective anti-viral treatments for coronavirus disease 2019 (COVID-19)-hospitalized patients with hypoxemia. Lymphopenia is a biomarker of disease severity usually present in patients who are hospitalized. Approaches to increasing lymphocytes exerting an anti-viral effect must be considered to treat these patients. Following our phase 1 study, we performed a phase 2 randomized multicenter clinical trial in which we evaluated the efficacy of the infusion of allogeneic off-the-shelf CD45RA- memory T cells containing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific T cells from convalescent donors plus the standard of care (SoC) versus just the SoC treatment. METHODS Eighty-four patients were enrolled in three Spanish centers. The patients were randomized into the infusion of 1 × 106/kg CD45RA- memory T cells or the SoC. We selected four unvaccinated donors based on the expression of interferon gamma SARS-CoV-2-specific response within the CD45RA- memory T cells and the most frequent human leukocyte antigen typing in the Spanish population. RESULTS We analyzed data from 81 patients. The primary outcome for recovery, defined as the proportion of participants in each group with normalization of fever, oxygen saturation sustained for at least 24 hours and lymphopenia recovery through day 14 or at discharge, was met for the experimental arm. We also observed faster lymphocyte recovery in the experimental group. We did not observe any treatment-related adverse events. CONCLUSIONS Adoptive cell therapy with off-the-shelf CD45RA- memory T cells containing SAR-CoV-2-specific T cells is safe, effective and accelerates lymphocyte recovery of patients with COVID-19 pneumonia and/or lymphopenia. TRIAL REGISTRATION NCT04578210.
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Affiliation(s)
- Cristina Ferreras
- Hospital La Paz Institute for Health Research, IdiPAZ, University Hospital La Paz, Madrid, Spain
| | - Clara Hernández-Blanco
- Internal Medicine Department, Hospital de Emergencias Enfermera Isabel Zendal, Madrid, Spain
| | | | - Karima Al-Akioui-Sanz
- Hospital La Paz Institute for Health Research, IdiPAZ, University Hospital La Paz, Madrid, Spain
| | - Marta Mora-Rillo
- Infectious Diseases Unit, Internal Medicine Department, University Hospital La Paz, Hospital La Paz Institute for Health Research, IdiPAZ, Consorcio Centro de Investigación Biomédica en Red CIBER-Infec, Madrid, Spain
| | - Fátima Ibáñez
- Internal Medicine Department, Hospital Puerta de Hierro, Madrid, Spain
| | | | - Jordi Cano-Ochando
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA; Centro Nacional de Microbiologia, Instituto de Salud Carlos III, 28220 Madrid, Spain; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Daniel Lozano-Ojalvo
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - María Jiménez-González
- Infectious Diseases Unit, Internal Medicine Department, University Hospital La Paz, Hospital La Paz Institute for Health Research, IdiPAZ, Consorcio Centro de Investigación Biomédica en Red CIBER-Infec, Madrid, Spain; Clinical Trials Unit (UCICEC) at Hospital La Paz Institute for Health Research, IdiPAZ, University Hospital La Paz, Madrid, Spain
| | - Rosa Goterris
- Hematology Department, Hospital Clinico Universitario, Valencia, Spain
| | | | - Raquel de Paz
- Hematology Department, University Hospital La Paz, Madrid, Spain
| | - Pilar Guerra-García
- Hospital La Paz Institute for Health Research, IdiPAZ, University Hospital La Paz, Madrid, Spain; Pediatric Hemato-Oncology Department, University Hospital La Paz, Madrid, Spain
| | | | - Pablo Molina
- Clinical Pharmacology Department, University Hospital La Paz, Madrid, Spain
| | | | - Beatriz Ruz-Caracuel
- Hospital La Paz Institute for Health Research, IdiPAZ, University Hospital La Paz, Madrid, Spain
| | - Alberto M Borobia
- Hospital La Paz Institute for Health Research, IdiPAZ, University Hospital La Paz, Madrid, Spain; Clinical Trials Unit (UCICEC) at Hospital La Paz Institute for Health Research, IdiPAZ, University Hospital La Paz, Madrid, Spain; Clinical Pharmacology Department, University Hospital La Paz, Madrid, Spain
| | - Antonio J Carcas
- Clinical Trials Unit (UCICEC) at Hospital La Paz Institute for Health Research, IdiPAZ, University Hospital La Paz, Madrid, Spain; Clinical Pharmacology Department, University Hospital La Paz, Madrid, Spain; Faculty of Medicine Universidad Autónoma de Madrid, Madrid, Spain
| | - Dolores Planelles
- Department of Histocompatibility, Centro de Transfusión de la Comunidad Valenciana, Valencia, Spain
| | - José Luis Vicario
- Histocompatibility, Centro de Transfusión de la Comunidad de Madrid, Madrid, Spain
| | - Miguel Ángel Moreno
- Histocompatibility, Centro de Transfusión de la Comunidad de Madrid, Madrid, Spain
| | - Antonio Balas
- Histocompatibility, Centro de Transfusión de la Comunidad de Madrid, Madrid, Spain
| | - Marta Llano
- Infectious Diseases Department, Hospital de Emergencias Enfermera Isabel Zendal, Madrid, Spain
| | - Andrea Llorente
- Infectious Diseases Department, Hospital de Emergencias Enfermera Isabel Zendal, Madrid, Spain
| | - Álvaro Del Balzo
- Emergency Unit, Internal Medicine Department, University Hospital La Paz, Madrid, Spain
| | - Carlos Cañada
- Emergency Unit, Internal Medicine Department, University Hospital La Paz, Madrid, Spain
| | - Miguel Ángel García
- Emergency Unit, Internal Medicine Department, University Hospital La Paz, Madrid, Spain
| | - María Elena Calvin
- Emergency Unit, Internal Medicine Department, University Hospital La Paz, Madrid, Spain
| | - Isabel Arenas
- Emergency Unit, Internal Medicine Department, University Hospital La Paz, Madrid, Spain
| | - Rebeca Pérez de Diego
- Laboratory of Immunogenetics of Human Diseases, IdiPAZ Institute for Health Research, La Paz University Hospital, Madrid, Spain; Innate Immunity Group, IdiPAZ Institute for Health Research, La Paz University Hospital, Madrid, Spain; Interdepartmental Group of Immunodeficiencies, Madrid, Spain
| | - Cristina Eguizábal
- Research Unit, Basque Centre for Blood Transfusion and Human Tissues, Osakidetza, Bizkaia, Spain; Biocruces Bizkaia Health Research Institute, Bizkaia, Spain
| | - Bernat Soria
- Health Research Institute-ISABIAL, Alicante University Hospital and Institute of Bioengineering, Miguel Hernández University, Alicante, Spain; University Pablo de Olavide, Sevilla, Spain
| | - Carlos Solano
- Hematology Department, Hospital Clinico Universitario, Valencia, Spain; Department of Medicine, University of Valencia, Valencia, Spain
| | - Antonio Pérez-Martínez
- Hospital La Paz Institute for Health Research, IdiPAZ, University Hospital La Paz, Madrid, Spain; Pediatric Hemato-Oncology Department, University Hospital La Paz, Madrid, Spain; Faculty of Medicine Universidad Autónoma de Madrid, Madrid, Spain.
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6
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Maiti AK. Therapeutic Challenges in COVID-19. Curr Mol Med 2024; 24:14-25. [PMID: 36567277 DOI: 10.2174/1566524023666221222162641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 10/18/2022] [Accepted: 11/10/2022] [Indexed: 12/27/2022]
Abstract
SARS-CoV2 is a novel respiratory coronavirus and, understanding its molecular mechanism is a prerequisite to developing effective treatment for COVID-19. This RNA genome-carrying virus has a protein coat with spikes (S) that attaches to the ACE2 receptor at the cell surface of human cells. Several repurposed drugs are used to treat COVID-19 patients that are proven to be largely unsuccessful or have limited success in reducing mortalities. Several vaccines are in use to reduce the viral load to prevent developing symptoms. Major challenges to their efficacy include the inability of antibody molecules to enter cells but remain effective in the bloodstream to kill the virus. The efficacy of vaccines also depends on their neutralizing ability to constantly evolve new virus strains due to novel mutations and evolutionary survival dynamics. Taken together, SARS-CoV2 antibody vaccines may not be very effective and other approaches based on genetic, genomic, and protein interactome could be fruitful to identify therapeutic targets to reduce disease-related mortalities.
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Affiliation(s)
- Amit K Maiti
- Department of Genetics and Genomics, Mydnavar, 28475 Greenfield Rd, Southfield MI 48076, USA
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7
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Hoseinnezhad T, Soltani N, Ziarati S, Behboudi E, Mousavi MJ. The role of HLA genetic variants in COVID-19 susceptibility, severity, and mortality: A global review. J Clin Lab Anal 2024; 38:e25005. [PMID: 38251811 PMCID: PMC10829690 DOI: 10.1002/jcla.25005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/15/2023] [Accepted: 01/02/2024] [Indexed: 01/23/2024] Open
Abstract
BACKGROUND The COVID-19 pandemic has had a profound global impact, with variations in susceptibility, severity, and mortality rates across different regions. While many factors can contribute to the spread and impact of the disease, specifically human leukocyte antigen (HLA) genetic variants have emerged as potential contributors to COVID-19 outcomes. METHODS In this comprehensive narrative review, we conducted a thorough literature search to identify relevant studies investigating the association between HLA genetic variants and COVID-19 outcomes. Additionally, we analyzed allelic frequency data from diverse populations to assess differences in COVID-19 incidence and severity. RESULTS Our review provides insights into the immunological mechanisms involving HLA-mediated responses to COVID-19 and highlights potential research directions and therapeutic interventions. We found evidence suggesting that certain HLA alleles, such as HLA-A02, may confer a lower risk of COVID-19, while others, like HLA-C04, may increase the risk of severe symptoms and mortality. Furthermore, our analysis of allele frequency distributions revealed significant variations among different populations. CONCLUSION Considering host genetic variations, particularly HLA genetic variants, is crucial for understanding COVID-19 susceptibility and severity. These findings have implications for personalized treatment and interventions based on an individual's genetic profile. However, further research is needed to unravel the precise mechanisms underlying the observed associations and explore the potential for targeted therapies or preventive measures based on HLA genetic variants.
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Affiliation(s)
- Taraneh Hoseinnezhad
- Student Research CommitteeBushehr University of Medical SciencesBushehrIran
- Department of Hematology, School of Para‐MedicineBushehr University of Medical SciencesBushehrIran
| | - Nasrin Soltani
- Student Research CommitteeBushehr University of Medical SciencesBushehrIran
- Department of Hematology, School of Para‐MedicineBushehr University of Medical SciencesBushehrIran
| | - Sarina Ziarati
- Student Research CommitteeBushehr University of Medical SciencesBushehrIran
| | - Emad Behboudi
- Department of Basic Medical SciencesKhoy University of Medical SciencesKhoyIran
| | - Mohammad Javad Mousavi
- Department of Hematology, School of Para‐MedicineBushehr University of Medical SciencesBushehrIran
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8
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Constantinescu-Bercu A, Lobiuc A, Căliman-Sturdza OA, Oiţă RC, Iavorschi M, Pavăl NE, Șoldănescu I, Dimian M, Covasa M. Long COVID: Molecular Mechanisms and Detection Techniques. Int J Mol Sci 2023; 25:408. [PMID: 38203577 PMCID: PMC10778767 DOI: 10.3390/ijms25010408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 12/25/2023] [Accepted: 12/26/2023] [Indexed: 01/12/2024] Open
Abstract
Long COVID, also known as post-acute sequelae of SARS-CoV-2 infection (PASC), has emerged as a significant health concern following the COVID-19 pandemic. Molecular mechanisms underlying the occurrence and progression of long COVID include viral persistence, immune dysregulation, endothelial dysfunction, and neurological involvement, and highlight the need for further research to develop targeted therapies for this condition. While a clearer picture of the clinical symptomatology is shaping, many molecular mechanisms are yet to be unraveled, given their complexity and high level of interaction with other metabolic pathways. This review summarizes some of the most important symptoms and associated molecular mechanisms that occur in long COVID, as well as the most relevant molecular techniques that can be used in understanding the viral pathogen, its affinity towards the host, and the possible outcomes of host-pathogen interaction.
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Affiliation(s)
- Adela Constantinescu-Bercu
- Department of Biomedical Sciences, Faculty of Medicine and Biological Sciences, “Ştefan cel Mare” University of Suceava, 720229 Suceava, Romania; (A.C.-B.); (O.A.C.-S.); (M.I.); (N.-E.P.); (M.C.)
| | - Andrei Lobiuc
- Department of Biomedical Sciences, Faculty of Medicine and Biological Sciences, “Ştefan cel Mare” University of Suceava, 720229 Suceava, Romania; (A.C.-B.); (O.A.C.-S.); (M.I.); (N.-E.P.); (M.C.)
| | - Olga Adriana Căliman-Sturdza
- Department of Biomedical Sciences, Faculty of Medicine and Biological Sciences, “Ştefan cel Mare” University of Suceava, 720229 Suceava, Romania; (A.C.-B.); (O.A.C.-S.); (M.I.); (N.-E.P.); (M.C.)
- Suceava Emergency Clinical County Hospital, 720224 Suceava, Romania
| | - Radu Cristian Oiţă
- Integrated Center for Research, Development and Innovation for Advanced Materials, Nanotechnologies, Manufacturing and Control Distributed Systems (MANSiD), Ştefan cel Mare University of Suceava, 720229 Suceava, Romania; (R.C.O.); (I.Ș.); (M.D.)
| | - Monica Iavorschi
- Department of Biomedical Sciences, Faculty of Medicine and Biological Sciences, “Ştefan cel Mare” University of Suceava, 720229 Suceava, Romania; (A.C.-B.); (O.A.C.-S.); (M.I.); (N.-E.P.); (M.C.)
| | - Naomi-Eunicia Pavăl
- Department of Biomedical Sciences, Faculty of Medicine and Biological Sciences, “Ştefan cel Mare” University of Suceava, 720229 Suceava, Romania; (A.C.-B.); (O.A.C.-S.); (M.I.); (N.-E.P.); (M.C.)
| | - Iuliana Șoldănescu
- Integrated Center for Research, Development and Innovation for Advanced Materials, Nanotechnologies, Manufacturing and Control Distributed Systems (MANSiD), Ştefan cel Mare University of Suceava, 720229 Suceava, Romania; (R.C.O.); (I.Ș.); (M.D.)
| | - Mihai Dimian
- Integrated Center for Research, Development and Innovation for Advanced Materials, Nanotechnologies, Manufacturing and Control Distributed Systems (MANSiD), Ştefan cel Mare University of Suceava, 720229 Suceava, Romania; (R.C.O.); (I.Ș.); (M.D.)
- Department of Computers, Electronics and Automation, Ştefan cel Mare University of Suceava, 720229 Suceava, Romania
| | - Mihai Covasa
- Department of Biomedical Sciences, Faculty of Medicine and Biological Sciences, “Ştefan cel Mare” University of Suceava, 720229 Suceava, Romania; (A.C.-B.); (O.A.C.-S.); (M.I.); (N.-E.P.); (M.C.)
- Department of Basic Medical Sciences, College of Osteopathic Medicine, Western University of Health Sciences, Pomona, CA 91711, USA
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9
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Lerner A, Benzvi C, Vojdani A. HLA-DQ2/8 and COVID-19 in Celiac Disease: Boon or Bane. Microorganisms 2023; 11:2977. [PMID: 38138121 PMCID: PMC10745744 DOI: 10.3390/microorganisms11122977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/05/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
The SARS-CoV-2 pandemic continues to pose a global threat. While its virulence has subsided, it has persisted due to the continual emergence of new mutations. Although many high-risk conditions related to COVID-19 have been identified, the understanding of protective factors remains limited. Intriguingly, epidemiological evidence suggests a low incidence of COVID-19-infected CD patients. The present study explores whether their genetic background, namely, the associated HLA-DQs, offers protection against severe COVID-19 outcomes. We hypothesize that the HLA-DQ2/8 alleles may shield CD patients from SARS-CoV-2 and its subsequent effects, possibly due to memory CD4 T cells primed by previous exposure to human-associated common cold coronaviruses (CCC) and higher affinity to those allele's groove. In this context, we examined potential cross-reactivity between SARS-CoV-2 epitopes and human-associated CCC and assessed the binding affinity (BA) of these epitopes to HLA-DQ2/8. Using computational methods, we analyzed sequence similarity between SARS-CoV-2 and four distinct CCC. Of 924 unique immunodominant 15-mer epitopes with at least 67% identity, 37 exhibited significant BA to HLA-DQ2/8, suggesting a protective effect. We present various mechanisms that might explain the protective role of HLA-DQ2/8 in COVID-19-afflicted CD patients. If substantiated, these insights could enhance our understanding of the gene-environment enigma and viral-host relationship, guiding potential therapeutic innovations against the ongoing SARS-CoV-2 pandemic.
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Affiliation(s)
- Aaron Lerner
- The Zabludowicz Center for Autoimmune Diseases, Chaim Sheba Medical Center, Ramat Gan 5262160, Israel;
- Research Department, Ariel University, Ariel 4077625, Israel
| | - Carina Benzvi
- The Zabludowicz Center for Autoimmune Diseases, Chaim Sheba Medical Center, Ramat Gan 5262160, Israel;
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10
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Vanaga I, Kolesova O, Kolesovs A, Sture G, Hagina E, Storozenko J, Nikitina-Zake L, Viksna L. Association of human leukocyte antigen class II alleles with epithelial cell apoptosis and extracellular matrix production in acute COVID-19. Cent Eur J Immunol 2023; 48:322-329. [PMID: 38558559 PMCID: PMC10976658 DOI: 10.5114/ceji.2023.133684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 10/16/2023] [Indexed: 04/04/2024] Open
Abstract
Introduction Pathogenic mechanisms and long-term consequences of COVID-19 require attention in studies on SARS-CoV-2. The association of the severity of COVID-19 with genetic factors, such as human leukocyte antigen (HLA) genes, remains underexplored. Our study assessed the relationships between HLA class II alleles and COVID-19 severity and blood-based indicators of systemic inflammation and organ damage, serum markers of epithelial cell apoptosis such as caspase-cleaved CK18 fragment M30 (CK18-M30) and the extracellular matrix product hyaluronic acid (HA). Material and methods The study included 101 hospitalized COVID-19 patients (mean age 60 ±14 years). Clinical tests were performed at admission to the hospital. The levels of CK18-M30 and HA were detected in serum by enzyme-linked immunosorbent assay (ELISA). HLA typing was performed in HLA-DRB1, -DQA1, and -DQB1 loci by the polymerase chain reaction with low-resolution sequence-specific primers. Results Sixty-one patients had a non-severe and 40 had a severe or critical disease course (following the WHO definition). The severity was associated with older age, male gender, higher HA, CK18-M30, and some indicators of inflammation. Despite the lack of direct association between HLA alleles and the severity of COVID-19, the presence of HLA-DRB1*04 and 12 alleles in the genotype was associated with lowered or elevated HA, respectively. The HLA-DQB1*03:01 allele was associated with lowered CK18-M30, aspartate aminotransferase, and ferritin. In addition, HLA-DQB1*06:01 was associated with elevated alanine aminotransferase. Conclusions Associations of HLA class II alleles with markers of epithelial cell apoptosis and extracellular matrix production indirectly support the influence of HLA genes on acute COVID-19 severity.
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Affiliation(s)
- Ieva Vanaga
- Riga Stradins University, Riga, Latvia
- Riga East Clinical University Hospital, Riga, Latvia
| | | | | | - Gunta Sture
- Riga Stradins University, Riga, Latvia
- Riga East Clinical University Hospital, Riga, Latvia
| | | | | | | | - Ludmila Viksna
- Riga Stradins University, Riga, Latvia
- Riga East Clinical University Hospital, Riga, Latvia
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11
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Ni C, Han Y, Wang Y, Ma T, Sha D, Xu Y, Cao W, Gao S. Human HLA prolongs the host inflammatory response in Streptococcus suis serotype 2 infection compared to mouse H2 molecules. Front Cell Infect Microbiol 2023; 13:1285055. [PMID: 38035330 PMCID: PMC10682707 DOI: 10.3389/fcimb.2023.1285055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 10/26/2023] [Indexed: 12/02/2023] Open
Abstract
Streptococcus suis (S. suis) is widely acknowledged as a significant zoonotic pathogen in Southeast Asia and China, which has led to a substantial number of fatalities in both swine and humans. Despite the prevalent use of mice as the primary animal model to study S. suis pathogenesis, the substantial differences in the major histocompatibility complex (MHC) between humans and mice underscore the ongoing exploration for a more suitable and effective animal model. In this study, humanized transgenic HLA-A11/DR1 genotypes mice were used to evaluate the differences between humanized HLA and murine H2 in S. suis infection. Following intravenous administration of S. suis suspensions, we investigated bacterial load, cytokine profiles, pathological alterations, and immune cell recruitment in both Wild-type (WT) and humanized mice across different post-infection time points. Relative to WT mice, humanized mice exhibited heightened pro-inflammatory cytokines, exacerbated tissue damage, increased granulocyte recruitment with impaired resolution, notably more pronounced during the late infection stage. Additionally, our examination of bacterial clearance rates suggests that HLA-A11/DR1 primarily influences cell recruitment and mitochondrial reactive oxygen species (ROS) production, which affects the bacterial killing capacity of macrophages in the late stage of infection. The reduced IL-10 production and lower levels of regulatory T cells in humanized mice could underlie their compromised resolution ability. Intervention with IL-10 promotes bacterial clearance and inflammatory regression in the late stages of infection in transgenic mice. Our findings underscore the heightened sensitivity of HLA-A11/DR1 mice with impaired resolution to S. suis infection, effectively mirroring the immune response seen in humans during infection. The humanized HLA-A11/DR1 mice could serve as an optimal animal model for investigating the pathogenic and therapeutic mechanisms associated with sepsis and other infectious diseases.
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Affiliation(s)
- Chengpei Ni
- The Affiliated Wuxi Center for Disease Control and Prevention of Nanjing Medical University, Wuxi Center for Disease Control and Prevention, Wuxi, China
| | - Yi Han
- The Affiliated Wuxi Center for Disease Control and Prevention of Nanjing Medical University, Wuxi Center for Disease Control and Prevention, Wuxi, China
| | - Yajing Wang
- The Affiliated Wuxi Center for Disease Control and Prevention of Nanjing Medical University, Wuxi Center for Disease Control and Prevention, Wuxi, China
| | - Ting Ma
- School of Public Health, Nanjing Medical University, Nanjing, China
| | - Dan Sha
- The Affiliated Wuxi Center for Disease Control and Prevention of Nanjing Medical University, Wuxi Center for Disease Control and Prevention, Wuxi, China
| | - Yanan Xu
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Wenting Cao
- The Affiliated Wuxi Center for Disease Control and Prevention of Nanjing Medical University, Wuxi Center for Disease Control and Prevention, Wuxi, China
| | - Song Gao
- The Affiliated Wuxi Center for Disease Control and Prevention of Nanjing Medical University, Wuxi Center for Disease Control and Prevention, Wuxi, China
- Wuxi Medical Center, Nanjing Medical University, Wuxi, China
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12
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Balas A, Moreno-Hidalgo MÁ, de la Calle-Prieto F, Vicario JL, Arsuaga M, Trigo E, de Miguel-Buckley R, Bellón T, Díaz-Menéndez M. Coronavirus-19 disease risk and protective factors associated with HLA/KIR polymorphisms in Ecuadorian patients residing in Madrid. Hum Immunol 2023; 84:571-577. [PMID: 37777360 DOI: 10.1016/j.humimm.2023.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 09/20/2023] [Accepted: 09/20/2023] [Indexed: 10/02/2023]
Abstract
BACKGROUND Immigrants represented 21.8% of cases in a Spanish cohort of hospitalised patients with COVID-19, a proportion exceeding the percentage of immigrants in that area's total population. Among the ethnic-related genetic risk factors for COVID-19, human leukocyte antigen (HLA) genotypes in diverse populations might bias the response to SARS-CoV-2 infection and/or progression. Similarly, genetic differences in natural killer-activating and inhibitory receptors could play a role in the immune system's response to the viral infection. METHODS We characterised HLA alleles and KIR genes in 52 Ecuadorian patients hospitalised for moderate and severe COVID-19 and 87 Ecuadorian controls from the general population living in the same area. RESULTS There was a significantly increased frequency of the HLA-B*39 antigen and the activating KIR2DS4 receptor in the presence of its HLA-C*04 ligand in the COVID-19 group when compared with the control group. In contrast, there was a significant reduction in the frequency of carriers of KIR2DL1 and of the KIR3DL1/Bw4 receptor/ligand combination among COVID-19 group. On the other hand, HLA-A*24:02 and HLA-DRB1*09:01 alleles showed significantly lower frequencies specifically in the severe COVID-19 group. CONCLUSION HLA-B*39 alleles might be genetic risk factors for developing COVID-19 in Ecuadorian individuals. In the presence of its ligand C*04, the natural killer-activating receptor KIR2DS4 might also increase the risk of developing COVID-19, while, in the presence of HLA-Bw4 alleles, the inhibitory receptor KIR3DL1 might play a protective role. Patients with COVID-19 who carry HLA-A*24:02 and HLA-DRB1*09:01 alleles might be protected against more severe forms of COVID-19.
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Affiliation(s)
- Antonio Balas
- Histocompatibility Unit, Centro de Transfusion de la Comunidad de Madrid, Madrid, Spain
| | | | - Fernando de la Calle-Prieto
- National Referral Unit for Imported Tropical Diseases and Travel Medicine, Infectious Diseases Department, Hospital Universitario La Paz-Carlos III, IdiPAZ, CIBERINFEC, Madrid, Spain
| | - José Luis Vicario
- Histocompatibility Unit, Centro de Transfusion de la Comunidad de Madrid, Madrid, Spain
| | - Marta Arsuaga
- National Referral Unit for Imported Tropical Diseases and Travel Medicine, Infectious Diseases Department, Hospital Universitario La Paz-Carlos III, IdiPAZ, CIBERINFEC, Madrid, Spain
| | - Elena Trigo
- National Referral Unit for Imported Tropical Diseases and Travel Medicine, Infectious Diseases Department, Hospital Universitario La Paz-Carlos III, IdiPAZ, CIBERINFEC, Madrid, Spain
| | - Rosa de Miguel-Buckley
- National Referral Unit for Imported Tropical Diseases and Travel Medicine, Infectious Diseases Department, Hospital Universitario La Paz-Carlos III, IdiPAZ, CIBERINFEC, Madrid, Spain
| | - Teresa Bellón
- Institute for Health Research Hospital Universitario La Paz (IdiPAZ), Madrid, Spain.
| | - Marta Díaz-Menéndez
- National Referral Unit for Imported Tropical Diseases and Travel Medicine, Infectious Diseases Department, Hospital Universitario La Paz-Carlos III, IdiPAZ, CIBERINFEC, Madrid, Spain
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13
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Li Y, Han L, Li P, Ge J, Xue Y, Chen L. Potential network markers and signaling pathways for B cells of COVID-19 based on single-cell condition-specific networks. BMC Genomics 2023; 24:619. [PMID: 37853311 PMCID: PMC10583333 DOI: 10.1186/s12864-023-09719-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 10/05/2023] [Indexed: 10/20/2023] Open
Abstract
To explore the potential network markers and related signaling pathways of human B cells infected by COVID-19, we performed standardized integration and analysis of single-cell sequencing data to construct conditional cell-specific networks (CCSN) for each cell. Then the peripheral blood cells were clustered and annotated based on the conditional network degree matrix (CNDM) and gene expression matrix (GEM), respectively, and B cells were selected for further analysis. Besides, based on the CNDM of B cells, the hub genes and 'dark' genes (a gene has a significant difference between case and control samples not in a gene expression level but in a conditional network degree level) closely related to COVID-19 were revealed. Interestingly, some of the 'dark' genes and differential degree genes (DDGs) encoded key proteins in the JAK-STAT pathway, which had antiviral effects. The protein p21 encoded by the 'dark' gene CDKN1A was a key regulator for the COVID-19 infection-related signaling pathway. Elevated levels of proteins encoded by some DDGs were directly related to disease severity of patients with COVID-19. In short, the proteins encoded by 'dark' genes complement some missing links in COVID-19 and these signaling pathways played an important role in the growth and activation of B cells.
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Affiliation(s)
- Ying Li
- School of Mathematics and Statistics, Henan University of Science and Technology, Luoyang, 471023, China
- Longmen Laboratory, Luoyang, 471003, Henan, China
| | - Liqin Han
- School of Mathematics and Statistics, Henan University of Science and Technology, Luoyang, 471023, China
- Longmen Laboratory, Luoyang, 471003, Henan, China
| | - Peiluan Li
- School of Mathematics and Statistics, Henan University of Science and Technology, Luoyang, 471023, China.
- Longmen Laboratory, Luoyang, 471003, Henan, China.
| | - Jing Ge
- Shanghai Immune Therapy Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200032, China
| | - Yun Xue
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Luonan Chen
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 201100, China.
- Key Laboratory of Systems Health Science of Zhejiang Province, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310000, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201100, China.
- West China Biomedical Big Data Center, Med-X Center for Informatics, West China Hospital, Sichuan University, Chengdu, 610041, China.
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14
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Boquett JA, Vianna FSL, Fagundes NJR, Schroeder L, Barbian M, Zagonel-Oliveira M, Andreis TF, Pôrto LCMS, Chies JAB, Schuler-Faccini L, Ashton-Prolla P, Rosset C. HLA haplotypes and differential regional mortality caused by COVID-19 in Brazil: an ecological study based on a large bone marrow donor bank dataset. AN ACAD BRAS CIENC 2023; 95:e20220801. [PMID: 37851747 DOI: 10.1590/0001-3765202320220801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 10/19/2022] [Indexed: 10/20/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) mortality rates varied among the states of Brazil during the course of the pandemics. The human leukocyte antigen (HLA) is a critical component of the antigen presentation pathway. Individuals with different HLA genotypes may trigger different immune responses against pathogens, which could culminate in different COVID-19 responses. HLA genotypes are variable, especially in the highly admixed Brazilian population. In this ecological study, we aimed to investigate the correlation between HLA haplotypes and the different regional distribution of COVID-19 mortality in Brazil. HLA data was obtained from 4,148,713 individuals registered in The Brazilian Voluntary Bone Marrow Donors Registry. COVID-19 data was retrieved from epidemiological bulletins issued by State Health Secretariats via Brazil's Ministry of Health from February/2020 to July/2022. We found a positive significant correlation between the HLA-A*01~B*08~DRB1*03 haplotype and COVID-19 mortality rates when we analyzed data from 26 states and the Federal District. This result indicates that the HLA-A*01~B*08~DRB1*03 haplotype may represent an additional risk factor for dying due to COVID-19. This haplotype should be further studied in other populations for a better understanding of the variation in COVID-19 outcomes across the world.
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Affiliation(s)
- Juliano André Boquett
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Avenida Bento Gonçalves, 9500, Agronomia, 91501-970 Porto Alegre, RS, Brazil
- Programa de Pós-Graduação em Saúde da Criança e do Adolescente, Universidade Federal do Rio Grande do Sul, Faculdade de Medicina, Rua Ramiro Barcelos, 2400, Santa Cecília, 90035-002 Porto Alegre, RS, Brazil
| | - Fernanda S L Vianna
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Avenida Bento Gonçalves, 9500, Agronomia, 91501-970 Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Rua Ramiro Barcelos, 2350, Santa Cecília, 90035-903 Porto Alegre, RS, Brazil
| | - Nelson J R Fagundes
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Avenida Bento Gonçalves, 9500, Agronomia, 91501-970 Porto Alegre, RS, Brazil
- Programa de Pós-Graduação em Biologia Animal, Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Avenida Bento Gonçalves, 9500, Agronomia, 91501-970 Porto Alegre, RS, Brazil
| | - Lucas Schroeder
- Programa de Pós-Graduação em Computação Aplicada, Universidade do Vale do Rio dos Sinos, Laboratório de Visualização Avançada (VIZLab), Avenida Unisinos, 950, Cristo Rei, 93022-750 São Leopoldo, RS, Brazil
| | - Marcia Barbian
- Universidade Federal do Rio Grande do Sul, Departamento de Estatística, Instituto de Matemática e Estatística, Avenida Bento Gonçalves, 9500, Agronomia, 91501-970 Porto Alegre, RS, Brazil
| | - Marcelo Zagonel-Oliveira
- Programa de Pós-Graduação em Computação Aplicada, Universidade do Vale do Rio dos Sinos, Laboratório de Visualização Avançada (VIZLab), Avenida Unisinos, 950, Cristo Rei, 93022-750 São Leopoldo, RS, Brazil
| | - Tiago F Andreis
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Avenida Bento Gonçalves, 9500, Agronomia, 91501-970 Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Rua Ramiro Barcelos, 2350, Santa Cecília, 90035-903 Porto Alegre, RS, Brazil
| | - Luis Cristóvão M S Pôrto
- Universidade Estadual do Rio de Janeiro, Laboratório de Histocompatibilidade e Criopreservação, Rua São Francisco Xavier, 524, Maracanã, 20550-013 Rio de Janeiro, RJ, Brazil
| | - José Artur B Chies
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Avenida Bento Gonçalves, 9500, Agronomia, 91501-970 Porto Alegre, RS, Brazil
| | - Lavinia Schuler-Faccini
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Avenida Bento Gonçalves, 9500, Agronomia, 91501-970 Porto Alegre, RS, Brazil
- Programa de Pós-Graduação em Saúde da Criança e do Adolescente, Universidade Federal do Rio Grande do Sul, Faculdade de Medicina, Rua Ramiro Barcelos, 2400, Santa Cecília, 90035-002 Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre, Serviço de Genética Médica, Rua Ramiro Barcelos, 2350, Santa Cecília, 90035-903 Porto Alegre, RS, Brazil
- Instituto Nacional de Genética Médica Populacional (iNaGeMP), Rua Ramiro Barcelos, 2350, Santa Cecília, 90035-903 Porto Alegre, RS, Brazil
| | - Patricia Ashton-Prolla
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Avenida Bento Gonçalves, 9500, Agronomia, 91501-970 Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Rua Ramiro Barcelos, 2350, Santa Cecília, 90035-903 Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre, Serviço de Genética Médica, Rua Ramiro Barcelos, 2350, Santa Cecília, 90035-903 Porto Alegre, RS, Brazil
| | - Clévia Rosset
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Rua Ramiro Barcelos, 2350, Santa Cecília, 90035-903 Porto Alegre, RS, Brazil
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15
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Witney MJ, Purcell AW, Tscharke DC. Need to know which MHCs protect against COVID? There's an App for that! Immunol Cell Biol 2023; 101:789-792. [PMID: 37638731 DOI: 10.1111/imcb.12680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2023]
Abstract
In this article, we discuss the recent observation by Augusto et al. made using a novel mobile phone application-based COVID-19 Citizen Science Study that an HLA genetic variant, HLA-B*15:01, is associated with asymptomatic SARS-CoV-2 infection. To explain this association, Augusto et al. describe a cross-reactive memory CD8+ T-cell response in HLA-B*15:01+ SARS-CoV-2 unexposed individuals that retains high avidity for two structurally conserved epitopes found in SARS-CoV-2 and seasonal coronavirus strains. These observations provide an insight into potential molecular determinants that facilitate rapid, early clearance of virus.
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Affiliation(s)
- Matthew J Witney
- Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Anthony W Purcell
- Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - David C Tscharke
- John Curtin School of Medical Research, The Australian National University, Acton, ACT, Australia
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16
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Rottmayer K, Loeffler-Wirth H, Gruenewald T, Doxiadis I, Lehmann C. Individual Immune Response to SARS-CoV-2 Infection-The Role of Seasonal Coronaviruses and Human Leukocyte Antigen. BIOLOGY 2023; 12:1293. [PMID: 37887003 PMCID: PMC10603889 DOI: 10.3390/biology12101293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/24/2023] [Accepted: 09/25/2023] [Indexed: 10/28/2023]
Abstract
During the coronavirus pandemic, evidence is growing that the severity, susceptibility and host immune response to SARS-CoV-2 infection can be highly variable. Several influencing factors have been discussed. Here, we investigated the humoral immune response against SARS-CoV-2 spike, S1, S2, the RBD, nucleocapsid moieties and S1 of seasonal coronaviruses: hCoV-229E, hCoV-HKU1, hCoV-NL63 and hCoV-OC43, as well as MERS-CoV and SARS-CoV, in a cohort of 512 individuals. A bead-based multiplex assay allowed simultaneous testing for all the above antigens and the identification of different antibody patterns. Then, we correlated these patterns with 11 HLA loci. Regarding the seasonal coronaviruses, we found a moderate negative correlation between antibody levels against hCoV-229E, hCoV-HKU1 and hCoV-NL63 and the SARS-CoV-2 antigens. This could be an indication of the original immunological imprinting. High and low antibody response patterns were distinguishable, demonstrating the individuality of the humoral response towards the virus. An immunogenetical factor associated with a high antibody response (formation of ≥4 different antibodies) was the presence of HLA A*26:01, C*02:02 and DPB1*04:01 alleles, whereas the HLA alleles DRB3*01:01, DPB1*03:01 and DB1*10:01 were enriched in low responders. A better understanding of this variable immune response could enable more individualized protective measures.
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Affiliation(s)
- Karla Rottmayer
- Laboratory for Transplantation Immunology, University Hospital Leipzig, Johannisallee 32, 04103 Leipzig, Germany
| | - Henry Loeffler-Wirth
- Interdisciplinary Centre for Bioinformatics, IZBI, Leipzig University, Haertelstr. 16–18, 04107 Leipzig, Germany
| | - Thomas Gruenewald
- Clinic for Infectious Diseases and Tropical Medicine, Klinikum Chemnitz, Flemmingstraße 2, 09116 Chemnitz, Germany
| | - Ilias Doxiadis
- Laboratory for Transplantation Immunology, University Hospital Leipzig, Johannisallee 32, 04103 Leipzig, Germany
| | - Claudia Lehmann
- Laboratory for Transplantation Immunology, University Hospital Leipzig, Johannisallee 32, 04103 Leipzig, Germany
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17
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Zhao X, Zhang M, Jia Y, Liu W, Li S, Gao C, Zhang L, Ni B, Ruan Z, Dong R. Featured immune characteristics of COVID-19 and systemic lupus erythematosus revealed by multidimensional integrated analyses. Inflamm Res 2023; 72:1877-1894. [PMID: 37725104 DOI: 10.1007/s00011-023-01791-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 08/16/2023] [Accepted: 08/19/2023] [Indexed: 09/21/2023] Open
Abstract
BACKGROUND Coronavirus disease 2019 (COVID-19) shares similar immune characteristics with autoimmune diseases like systemic lupus erythematosus (SLE). However, such associations have not yet been investigated at the single-cell level. METHODS We integrated and analyzed RNA sequencing results from different patients and normal controls from the GEO database and identified subsets of immune cells that might involve in the pathogenesis of SLE and COVID- 19. We also disentangled the characteristic alterations in cell and molecular subset proportions as well as gene expression patterns in SLE patients compared with COVID-19 patients. RESULTS Key immune characteristic genes (such as CXCL10 and RACK1) and multiple immune-related pathways (such as the coronavirus disease-COVID-19, T-cell receptor signaling, and MIF-related signaling pathways) were identified. We also highlighted the differences in peripheral blood mononuclear cells (PBMCs) between SLE and COVID-19 patients. Moreover, we provided an opportunity to comprehensively probe underlying B-cell‒cell communication with multiple ligand-receptor pairs (MIF-CD74+CXCR4, MIF-CD74+CD44) and the differentiation trajectory of B-cell clusters that is deemed to promote cell state transitions in COVID-19 and SLE. CONCLUSIONS Our results demonstrate the immune response differences and immune characteristic similarities, such as the cytokine storm, between COVID-19 and SLE, which might pivotally function in the pathogenesis of the two diseases and provide potential intervention targets for both diseases.
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Affiliation(s)
- Xingwang Zhao
- Department of Dermatology, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing, 400038, China
| | - Mengjie Zhang
- Department of Pathophysiology, College of High Altitude Military Medicine, Army Medical University (Third Military Medical University), Chongqing, 400038, China
| | - Yuying Jia
- Department of Dermatology, The 901th Hospital of the Joint Logistics Support Force of PLA, Affiliated to Anhui Medical University, Hefei, Anhui, China
- Division of Life Sciences and Medicine, Dermatology Department of the First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, 230001, Anhui, People's Republic of China
| | - Wenying Liu
- Department of Dermatology, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing, 400038, China
| | - Shifei Li
- Department of Dermatology, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing, 400038, China
| | - Cuie Gao
- Department of Dermatology, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing, 400038, China
| | - Lian Zhang
- Department of Dermatology, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing, 400038, China
| | - Bing Ni
- Department of Pathophysiology, College of High Altitude Military Medicine, Army Medical University (Third Military Medical University), Chongqing, 400038, China
| | - Zhihua Ruan
- Department of Oncology and Southwest Cancer Center, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing, 400038, China.
| | - Rui Dong
- Department of Pathophysiology, College of High Altitude Military Medicine, Army Medical University (Third Military Medical University), Chongqing, 400038, China.
- Chongqing International Institute for Immunology, Chongqing, 401320, China.
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18
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Jensen TSR, Fugleholm K, Ekstrøm CT, Bruunsgaard H. Inflammatory human leucocyte antigen genotypes are not a risk factor in chronic subdural hematoma development. Acta Neurochir (Wien) 2023; 165:2399-2405. [PMID: 37550524 DOI: 10.1007/s00701-023-05745-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 07/26/2023] [Indexed: 08/09/2023]
Abstract
BACKGROUND Chronic subdural hematoma (CSDH) pathophysiology has undergone a paradigm shift from being regarded as solely traumatic to be driven mainly by inflammation. Human leucocyte antigen (HLA) is a gene complex involved in antigen processing and presentation to T lymphocytes, thereby mediating the adaptive immune responses. As specific HLA profiles are associated with inflammatory diseases, patients with a specific HLA profile may have a lower threshold for subdural inflammation, and therefore are predisposed for CSDH development. We hypothesized that (1) CSDH patients have a specific HLA profile compared to a Danish background population, and (2) patients with recurrent CSDH have a specific HLA profile compared to CSDH patients without recurrent CSDH. METHODS Three specific HLA class II haplotypes known to drive inflammatory-mediated diseases were determined in 68 patients with CSDH. The distribution of these three haplotypes in our CSDH population was compared to a Danish population of blood donors using Monte Carlo Pearson's chi-square test. Furthermore, the distribution of the haplotypes was compared between CSDH patients with and without recurrent CSDH. RESULTS We found no significant association between either of the haplotypes and the risk of CSDH, and neither of the haplotypes were associated with increased risk of CSDH recurrence. CONCLUSION This study did not show an association between selected HLA class II haplotypes and the risk of CSDH or recurrence of CSDH compared with a healthy background population.
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Affiliation(s)
- Thorbjørn Søren Rønn Jensen
- Department of Neurosurgery, The Neuroscience Centre, Copenhagen University Hospital, Rigshospitalet, Inge Lehmanns Vej 6, 2100, Copenhagen Ø, Denmark.
| | - Kåre Fugleholm
- Department of Neurosurgery, The Neuroscience Centre, Copenhagen University Hospital, Rigshospitalet, Inge Lehmanns Vej 6, 2100, Copenhagen Ø, Denmark
| | - Claus Thorn Ekstrøm
- Section of Biostatistics, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Helle Bruunsgaard
- Department of Clinical Immunology 7631, University Hospital of Copenhagen - Rigshospitalet and Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
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19
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Augusto DG, Murdolo LD, Chatzileontiadou DSM, Sabatino JJ, Yusufali T, Peyser ND, Butcher X, Kizer K, Guthrie K, Murray VW, Pae V, Sarvadhavabhatla S, Beltran F, Gill GS, Lynch KL, Yun C, Maguire CT, Peluso MJ, Hoh R, Henrich TJ, Deeks SG, Davidson M, Lu S, Goldberg SA, Kelly JD, Martin JN, Vierra-Green CA, Spellman SR, Langton DJ, Dewar-Oldis MJ, Smith C, Barnard PJ, Lee S, Marcus GM, Olgin JE, Pletcher MJ, Maiers M, Gras S, Hollenbach JA. A common allele of HLA is associated with asymptomatic SARS-CoV-2 infection. Nature 2023; 620:128-136. [PMID: 37468623 PMCID: PMC10396966 DOI: 10.1038/s41586-023-06331-x] [Citation(s) in RCA: 53] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 06/15/2023] [Indexed: 07/21/2023]
Abstract
Studies have demonstrated that at least 20% of individuals infected with SARS-CoV-2 remain asymptomatic1-4. Although most global efforts have focused on severe illness in COVID-19, examining asymptomatic infection provides a unique opportunity to consider early immunological features that promote rapid viral clearance. Here, postulating that variation in the human leukocyte antigen (HLA) loci may underly processes mediating asymptomatic infection, we enrolled 29,947 individuals, for whom high-resolution HLA genotyping data were available, in a smartphone-based study designed to track COVID-19 symptoms and outcomes. Our discovery cohort (n = 1,428) comprised unvaccinated individuals who reported a positive test result for SARS-CoV-2. We tested for association of five HLA loci with disease course and identified a strong association between HLA-B*15:01 and asymptomatic infection, observed in two independent cohorts. Suggesting that this genetic association is due to pre-existing T cell immunity, we show that T cells from pre-pandemic samples from individuals carrying HLA-B*15:01 were reactive to the immunodominant SARS-CoV-2 S-derived peptide NQKLIANQF. The majority of the reactive T cells displayed a memory phenotype, were highly polyfunctional and were cross-reactive to a peptide derived from seasonal coronaviruses. The crystal structure of HLA-B*15:01-peptide complexes demonstrates that the peptides NQKLIANQF and NQKLIANAF (from OC43-CoV and HKU1-CoV) share a similar ability to be stabilized and presented by HLA-B*15:01. Finally, we show that the structural similarity of the peptides underpins T cell cross-reactivity of high-affinity public T cell receptors, providing the molecular basis for HLA-B*15:01-mediated pre-existing immunity.
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Affiliation(s)
- Danillo G Augusto
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, NC, USA
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Lawton D Murdolo
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
| | - Demetra S M Chatzileontiadou
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Joseph J Sabatino
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | - Tasneem Yusufali
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | - Noah D Peyser
- Division of Cardiology, Department of Medicine, University of California, San Francisco, CA, USA
| | - Xochitl Butcher
- Division of Cardiology, Department of Medicine, University of California, San Francisco, CA, USA
| | - Kerry Kizer
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | - Karoline Guthrie
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | - Victoria W Murray
- Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Vivian Pae
- Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Sannidhi Sarvadhavabhatla
- Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Fiona Beltran
- Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Gurjot S Gill
- Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Kara L Lynch
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Cassandra Yun
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Colin T Maguire
- Clinical and Translational Science Institute, University of Utah, Salt Lake City, UT, USA
| | - Michael J Peluso
- Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Rebecca Hoh
- Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Timothy J Henrich
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Steven G Deeks
- Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Michelle Davidson
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Scott Lu
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - Sarah A Goldberg
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - J Daniel Kelly
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
- F.I. Proctor Foundation, University of California, San Francisco, CA, USA
| | - Jeffrey N Martin
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - Cynthia A Vierra-Green
- CIBMTR (Center for International Blood and Marrow Transplant Research), National Marrow Donor Program/Be The Match, Minneapolis, MN, USA
| | - Stephen R Spellman
- CIBMTR (Center for International Blood and Marrow Transplant Research), National Marrow Donor Program/Be The Match, Minneapolis, MN, USA
| | | | - Michael J Dewar-Oldis
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
| | - Corey Smith
- QIMR Berghofer Centre for Immunotherapy and Vaccine Development Brisbane, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Peter J Barnard
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
| | - Sulggi Lee
- Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Gregory M Marcus
- Division of Cardiology, Department of Medicine, University of California, San Francisco, CA, USA
| | - Jeffrey E Olgin
- Division of Cardiology, Department of Medicine, University of California, San Francisco, CA, USA
| | - Mark J Pletcher
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
- Division of General Internal Medicine, University of California, San Francisco, CA, USA
| | - Martin Maiers
- CIBMTR (Center for International Blood and Marrow Transplant Research), National Marrow Donor Program/Be The Match, Minneapolis, MN, USA
| | - Stephanie Gras
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Jill A Hollenbach
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA.
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA.
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20
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Di Salvatore V, Crispino E, Maleki A, Nicotra G, Russo G, Pappalardo F. Computational identification of differentially-expressed genes as suggested novel COVID-19 biomarkers: A bioinformatics analysis of expression profiles. Comput Struct Biotechnol J 2023; 21:3339-3354. [PMID: 37347079 PMCID: PMC10259169 DOI: 10.1016/j.csbj.2023.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 06/07/2023] [Accepted: 06/07/2023] [Indexed: 06/23/2023] Open
Abstract
COVID-19 was declared a pandemic in March 2020, and since then, it has not stopped spreading like wildfire in almost every corner of the world, despite the many efforts made to stem its spread. SARS-CoV-2 has one of the biggest genomes among RNA viruses and presents unique characteristics that differentiate it from other coronaviruses, making it even more challenging to find a cure or vaccine that is efficient enough. This work aims, using RNA sequencing (RNA-Seq) data, to evaluate whether the expression of specific human genes in the host can vary in different grades of disease severity and to determine the molecular origins of the differences in response to SARS-CoV-2 infection in different patients. In addition to quantifying gene expression, data coming from RNA-Seq allow for the discovery of new transcripts, the identification of alternative splicing events, the detection of allele-specific expression, and the detection of post-transcriptional alterations. For this reason, we performed differential expression analysis on different expression profiles of COVID-19 patients, using RNA-Seq data coming from NCBI public repository, and we obtained the lists of all differentially expressed genes (DEGs) emerging from 7 experimental conditions. We performed a Gene Set Enrichment Analysis (GSEA) on these genes to find possible correlations between DEGs and known disease phenotypes. We mainly focused on DEGs coming out from the analysis of the contrasts involving severe conditions to infer any possible relation between a worsening of the clinical picture and an over-representation of specific genes. Based on the obtained results, this study indicates a small group of genes that result up-regulated in the severe form of the disease. EXOSC5, MESD, REXO2, and TRMT2A genes are not differentially expressed or not present in the other conditions, being for that reason, good biomarkers candidates for the severe form of COVID-19 disease. The use of specific over-expressed genes, whether up-regulated or down-regulated, which have an individual role in each different condition of COVID-19 as a biomarker, can assist in early diagnosis.
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Affiliation(s)
| | - Elena Crispino
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Avisa Maleki
- Department of Mathematics and Computer Science, University of Catania, Catania, Italy
| | - Giulia Nicotra
- Department of Drug and Health Sciences, University of Catania, Catania, Italy
| | - Giulia Russo
- Department of Drug and Health Sciences, University of Catania, Catania, Italy
- Mimesis SRL, Catania, Italy
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21
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Brand M, Keşmir C. Evolution of SARS-CoV-2-specific CD4 + T cell epitopes. Immunogenetics 2023; 75:283-293. [PMID: 36719467 PMCID: PMC9887569 DOI: 10.1007/s00251-023-01295-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 01/10/2023] [Indexed: 02/01/2023]
Abstract
Vaccination clearly decreases coronavirus disease 2019 (COVID-19) mortality; however, they also impose selection pressure on the virus, which promotes the evolution of immune escape variants. For example, despite the high vaccination level in especially Western countries, the Omicron variant caused millions of breakthrough infections, suggesting that the highly mutated spike protein in the Omicron variant can escape antibody immunity much more efficiently than the other variants of concern (VOCs). In this study, we investigated the resistance/susceptibility of T helper cell responses that are necessary for generating efficient long-lasting antibody immunity, in several VOCs. By predicting T helper cell epitopes on the spike protein for most common HLA-DRB1 alleles worldwide, we found that although most of high frequency HLA-DRB1 alleles have several potential T helper cell epitopes, few alleles like HLA-DRB1 13:01 and 11:01 are not predicted to have any significant T helper cell responses after vaccination. Using these predictions, a population based on realistic human leukocyte antigen-II (HLA-II) frequencies were simulated to visualize the T helper cell immunity on the population level. While a small fraction of this population had alarmingly little predicted CD4 T cell epitopes, the majority had several epitopes that should be enough to generate efficient B cell responses. Moreover, we show that VOC spike mutations hardly affect T helper epitopes and mainly occur in other residues of the spike protein. These results suggest that lack of long-lasting antibody responses is not likely due to loss of T helper cell epitopes in new VOCs.
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Affiliation(s)
- Marina Brand
- Theoretical Biology & Bioinformatics, Utrecht University, Utrecht, Netherlands
| | - Can Keşmir
- Theoretical Biology & Bioinformatics, Utrecht University, Utrecht, Netherlands.
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22
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Ahadova A, Witt J, Haupt S, Gallon R, Hüneburg R, Nattermann J, Ten Broeke S, Bohaumilitzky L, Hernandez-Sanchez A, Santibanez-Koref M, Jackson MS, Ahtiainen M, Pylvänäinen K, Andini K, Grolmusz VK, Möslein G, Dominguez-Valentin M, Møller P, Fürst D, Sijmons R, Borthwick GM, Burn J, Mecklin JP, Heuveline V, von Knebel Doeberitz M, Seppälä T, Kloor M. Is HLA type a possible cancer risk modifier in Lynch syndrome? Int J Cancer 2023; 152:2024-2031. [PMID: 36214792 DOI: 10.1002/ijc.34312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 09/02/2022] [Accepted: 09/16/2022] [Indexed: 11/05/2022]
Abstract
Lynch syndrome (LS) is the most common inherited cancer syndrome. It is inherited via a monoallelic germline variant in one of the DNA mismatch repair (MMR) genes. LS carriers have a broad 30% to 80% risk of developing various malignancies, and more precise, individual risk estimations would be of high clinical value, allowing tailored cancer prevention and surveillance. Due to MMR deficiency, LS cancers are characterized by the accumulation of frameshift mutations leading to highly immunogenic frameshift peptides (FSPs). Thus, immune surveillance is proposed to inhibit the outgrowth of MMR-deficient cell clones. Recent studies have shown that immunoediting during the evolution of MMR-deficient cancers leads to a counter-selection of highly immunogenic antigens. The immunogenicity of FSPs is dependent on the antigen presentation. One crucial factor determining antigen presentation is the HLA genotype. Hence, a LS carrier's HLA genotype plays an important role in the presentation of FSP antigens to the immune system, and may influence the likelihood of progression from precancerous lesions to cancer. To address the challenge of clarifying this possibility including diverse populations with different HLA types, we have established the INDICATE initiative (Individual cancer risk by HLA type, http://indicate-lynch.org/), an international network aiming at a systematic evaluation of the HLA genotype as a possible cancer risk modifier in LS. Here we summarize the current knowledge on the role of HLA type in cancer risk and outline future research directions to delineate possible association in the scenario of LS with genetically defined risk population and highly immunogenic tumors.
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Affiliation(s)
- Aysel Ahadova
- Department of Applied Tumor Biology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,Cooperation Unit Applied Tumor Biology, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Johannes Witt
- Department of Applied Tumor Biology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,Cooperation Unit Applied Tumor Biology, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Saskia Haupt
- Engineering Mathematics and Computing Lab (EMCL), Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Heidelberg, Germany.,Data Mining and Uncertainty Quantification (DMQ), Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
| | - Richard Gallon
- Translational and Clinical Research Institute, Newcastle University, International Centre for Life, Newcastle upon Tyne, UK
| | - Robert Hüneburg
- Department of Internal Medicine I, University Hospital Bonn, Bonn, Germany.,National Center for Hereditary Tumor Syndromes, University Hospital Bonn, Bonn, Germany
| | - Jacob Nattermann
- Department of Internal Medicine I, University Hospital Bonn, Bonn, Germany.,National Center for Hereditary Tumor Syndromes, University Hospital Bonn, Bonn, Germany
| | - Sanne Ten Broeke
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | - Lena Bohaumilitzky
- Department of Applied Tumor Biology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,Cooperation Unit Applied Tumor Biology, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Alejandro Hernandez-Sanchez
- Department of Applied Tumor Biology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,Cooperation Unit Applied Tumor Biology, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Mauro Santibanez-Koref
- Translational and Clinical Research Institute, Newcastle University, International Centre for Life, Newcastle upon Tyne, UK
| | - Michael S Jackson
- Translational and Clinical Research Institute, Newcastle University, International Centre for Life, Newcastle upon Tyne, UK
| | | | - Kirsi Pylvänäinen
- Department of Education and science, Nova Hospital, Jyväskylä, Finland
| | - Katarina Andini
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | - Vince Kornel Grolmusz
- Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary.,Hereditary Cancers Research Group, Hungarian Academy of Sciences-Semmelweis University, Budapest, Hungary
| | - Gabriela Möslein
- Department of Surgery, Ev. Krankenhaus Bethesda Hospital, Duisburg, Germany
| | - Mev Dominguez-Valentin
- Department of Tumor Biology, Institute of Cancer Research, The Norwegian Radium Hospital, Oslo, Norway
| | - Pål Møller
- Department of Tumor Biology, Institute of Cancer Research, The Norwegian Radium Hospital, Oslo, Norway
| | - Daniel Fürst
- Institute of Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Transfusion Service, Baden Wuerttemberg-Hessen, University Hospital Ulm, Ulm, Germany.,Institute of Transfusion Medicine, University of Ulm, Ulm, Germany
| | - Rolf Sijmons
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | - Gillian M Borthwick
- Translational and Clinical Research Institute, Newcastle University, International Centre for Life, Newcastle upon Tyne, UK
| | - John Burn
- Translational and Clinical Research Institute, Newcastle University, International Centre for Life, Newcastle upon Tyne, UK
| | - Jukka-Pekka Mecklin
- Faculty of Sport and Health Sciences, University of Jyväskylä, Jyväskylä, Finland.,Department of Surgery, Nova Hospital, Jyväskylä, Finland
| | - Vincent Heuveline
- Engineering Mathematics and Computing Lab (EMCL), Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Heidelberg, Germany.,Data Mining and Uncertainty Quantification (DMQ), Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
| | - Magnus von Knebel Doeberitz
- Department of Applied Tumor Biology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,Cooperation Unit Applied Tumor Biology, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Toni Seppälä
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland.,Department of Gastrointestinal Surgery, Helsinki University Central Hospital, Helsinki, Finland.,Applied Tumor Genomics Research Program, University of Helsinki, Helsinki, Finland
| | - Matthias Kloor
- Department of Applied Tumor Biology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,Cooperation Unit Applied Tumor Biology, German Cancer Research Centre (DKFZ), Heidelberg, Germany
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23
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Liu C, Zhang L, Chen J, Gao Y. Targeted capture enrichment and sequencing identifies HLA variants associated with the severity of COVID-19. Genes Genomics 2023; 45:451-456. [PMID: 36574143 PMCID: PMC9793816 DOI: 10.1007/s13258-022-01358-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 12/20/2022] [Indexed: 12/28/2022]
Abstract
BACKGROUND Coronavirus disease 2019 (COVID-19) is currently a global pandemic. The pathogenesis of severe COVID-19 has been widely investigated, but it is still unclear. Human leukocyte antigen (HLA) plays a central role in immune response, and its variants might be related to COVID-19 progression and severity. OBJECTIVE To investigate the hypothesis that individual HLA variations could alter the course of COVID-19 and might be associated with the severity of COVID-19. METHODS In this study, we conducted an HLA targeted capture enrichment and sequencing of severe COVID-19 patients matched to mild cases. A total of 16 COVID-19 patients, confirmed by SARS-CoV-2 viral RNA polymerase-chain-reaction (PCR) test and chest computed tomography (CT) scan, were enrolled in this study. The HLA targeted capture enrichment and sequencing were conducted. HLA typing was performed by comparing contigs with IPD-IMGT/HLA Database. RESULTS In this study, 139 four-digit resolution HLA alleles were acquired. The results showed that HLA-DRB3*01:01 allele was significantly associated with the severity of COVID-19 (odds ratio [OR] = 27.64, 95% confidence interval [CI] = 1.35-560.50, P = 0.0064). And HLA-K*01:01 might be a potential risk factor for COVID-19 severity (OR = 0.11, 95% CI = 0.017-0.66, P = 0.019), but HLA-K*01:02 might be a protective factor (OR = 7.50, 95% CI = 1.48-37.92, P = 0.019). CONCLUSION Three non-classical HLA alleles, including HLA-DRB3*01:01, HLA-K*01:01, HLA-K*01:02 were identified to be associated with the severity of COVID-19 by comparing mild and severe patients. The current findings would be helpful for exploring the influence of HLA gene polymorphisms on the development and severity of COVID-19.
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Affiliation(s)
- Chuanmiao Liu
- Department of Infectious Disease, The First Affiliated Hospital of Bengbu Medical College, Bengbu Medical College, Bengbu, China
- National Clinical Research Center for Infectious Diseases, First Affiliated Hospital of Bengbu Medical College, Bengbu Medical College, Bengbu, China
| | - Li Zhang
- Department of Infectious Disease, The First Affiliated Hospital of Bengbu Medical College, Bengbu Medical College, Bengbu, China
- National Clinical Research Center for Infectious Diseases, First Affiliated Hospital of Bengbu Medical College, Bengbu Medical College, Bengbu, China
| | - Jiasheng Chen
- Department of Infectious Disease, The First Affiliated Hospital of Bengbu Medical College, Bengbu Medical College, Bengbu, China
- National Clinical Research Center for Infectious Diseases, First Affiliated Hospital of Bengbu Medical College, Bengbu Medical College, Bengbu, China
| | - Yu Gao
- School of Life Science, Bengbu Medical College, Bengbu, China.
- Anhui Province Key Laboratory of Translational Cancer Research, Bengbu Medical College, Bengbu, China.
- School of Life Science, Anhui Province Key Laboratory of Translational Cancer Research, Bengbu Medical College, No. 2600 Donghai Road, Bengbu, 233030, China.
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24
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Brown B, Ojha V, Fricke I, Al-Sheboul SA, Imarogbe C, Gravier T, Green M, Peterson L, Koutsaroff IP, Demir A, Andrieu J, Leow CY, Leow CH. Innate and Adaptive Immunity during SARS-CoV-2 Infection: Biomolecular Cellular Markers and Mechanisms. Vaccines (Basel) 2023; 11:408. [PMID: 36851285 PMCID: PMC9962967 DOI: 10.3390/vaccines11020408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 02/01/2023] [Accepted: 02/04/2023] [Indexed: 02/16/2023] Open
Abstract
The coronavirus 2019 (COVID-19) pandemic was caused by a positive sense single-stranded RNA (ssRNA) severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, other human coronaviruses (hCoVs) exist. Historical pandemics include smallpox and influenza, with efficacious therapeutics utilized to reduce overall disease burden through effectively targeting a competent host immune system response. The immune system is composed of primary/secondary lymphoid structures with initially eight types of immune cell types, and many other subtypes, traversing cell membranes utilizing cell signaling cascades that contribute towards clearance of pathogenic proteins. Other proteins discussed include cluster of differentiation (CD) markers, major histocompatibility complexes (MHC), pleiotropic interleukins (IL), and chemokines (CXC). The historical concepts of host immunity are the innate and adaptive immune systems. The adaptive immune system is represented by T cells, B cells, and antibodies. The innate immune system is represented by macrophages, neutrophils, dendritic cells, and the complement system. Other viruses can affect and regulate cell cycle progression for example, in cancers that include human papillomavirus (HPV: cervical carcinoma), Epstein-Barr virus (EBV: lymphoma), Hepatitis B and C (HB/HC: hepatocellular carcinoma) and human T cell Leukemia Virus-1 (T cell leukemia). Bacterial infections also increase the risk of developing cancer (e.g., Helicobacter pylori). Viral and bacterial factors can cause both morbidity and mortality alongside being transmitted within clinical and community settings through affecting a host immune response. Therefore, it is appropriate to contextualize advances in single cell sequencing in conjunction with other laboratory techniques allowing insights into immune cell characterization. These developments offer improved clarity and understanding that overlap with autoimmune conditions that could be affected by innate B cells (B1+ or marginal zone cells) or adaptive T cell responses to SARS-CoV-2 infection and other pathologies. Thus, this review starts with an introduction into host respiratory infection before examining invaluable cellular messenger proteins and then individual immune cell markers.
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Affiliation(s)
| | | | - Ingo Fricke
- Independent Immunologist and Researcher, 311995 Lamspringe, Germany
| | - Suhaila A Al-Sheboul
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, Jordan University of Science and Technology, Irbid 22110, Jordan
- Department of Medical Microbiology, International School of Medicine, Medipol University-Istanbul, Istanbul 34810, Turkey
| | | | - Tanya Gravier
- Independent Researcher, MPH, San Francisco, CA 94131, USA
| | | | | | | | - Ayça Demir
- Faculty of Medicine, Afyonkarahisar University, Istanbul 03030, Turkey
| | - Jonatane Andrieu
- Faculté de Médecine, Aix–Marseille University, 13005 Marseille, France
| | - Chiuan Yee Leow
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, USM, Penang 11800, Malaysia
| | - Chiuan Herng Leow
- Institute for Research in Molecular Medicine, (INFORMM), Universiti Sains Malaysia, USM, Penang 11800, Malaysia
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25
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The Search of Association of HLA Class I and Class II Alleles with COVID-19 Mortality in the Russian Cohort. Int J Mol Sci 2023; 24:ijms24043068. [PMID: 36834479 PMCID: PMC9960097 DOI: 10.3390/ijms24043068] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/18/2023] [Accepted: 01/24/2023] [Indexed: 02/08/2023] Open
Abstract
HLA genes play a pivotal role in the immune response via presenting the pathogen peptides on the cell surface in a host organism. Here, we studied the association of HLA allele variants of class I (loci A, B, C) and class II (loci DRB1, DQB1, DPB1) genes with the outcome of COVID-19 infection. We performed high-resolution sequencing of class HLA I and class II genes based on the sample population of 157 patients who died from COVID-19 and 76 patients who survived despite severe symptoms. The results were further compared with HLA genotype frequencies in the control population represented by 475 people from the Russian population. Although the obtained data revealed no significant differences between the samples at a locus level, they allowed one to uncover a set of notable alleles potentially contributing to the COVID-19 outcome. Our results did not only confirm the previously discovered fatal role of age or association of DRB1*01:01:01G and DRB1*01:02:01G alleles with severe symptoms and survival, but also allowed us to single out the DQB1*05:03:01G allele and B*14:02:01G~C*08:02:01G haplotype, which were associated with survival. Our findings showed that not only separate allele, but also their haplotype, could serve as potential markers of COVID-19 outcome and be used during triage for hospital admission.
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26
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Yao M, Huang X, Guo Y, Zhao JV, Liu Z. Disentangling the common genetic architecture and causality of rheumatoid arthritis and systemic lupus erythematosus with COVID-19 outcomes: Genome-wide cross trait analysis and bidirectional Mendelian randomization study. J Med Virol 2023; 95:e28570. [PMID: 36762574 DOI: 10.1002/jmv.28570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/31/2023] [Accepted: 02/07/2023] [Indexed: 02/11/2023]
Abstract
Coronavirus Disease (COVID-19) may cause a dysregulation of the immune system and has complex relationships with multiple autoimmune diseases, including rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE). However, little is known about their common genetic architecture. Using the latest data from COVID-19 host genetics consortium and consortia on RA and SLE, we conducted a genome-wide cross-trait analysis to examine the shared genetic etiology between COVID-19 and RA/SLE and evaluated their causal associations using bidirectional Mendelian randomization (MR). The cross-trait meta-analysis identified 23, 28, and 10 shared genetic loci for severe COVID-19, COVID-19 hospitalization, and SARS-CoV-2 infection with RA, and 14, 17, and 7 shared loci with SLE, respectively. Co-localization analysis identified five causal variants in TYK2, IKZF3, PSORS1C1, and COG6 for COVID-19 with RA, and four in CRHR1, FUT2, and NXPE3 for COVID-19 with SLE, involved in immune function, angiogenesis and coagulation. Bidirectional MR analysis suggested RA is associated with a higher risk of COVID-19 hospitalization, and COVID-19 is not related to RA or SLE. Our novel findings improved the understanding of the genetic etiology shared by COVID-19, RA and SLE, and suggested an increased risk of COVID-19 hospitalization in people with higher genetic liability to RA.
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Affiliation(s)
- Minhao Yao
- Department of Statistics and Actuarial Science, The University of Hong Kong, Hong Kong, Hong Kong, China
| | - Xin Huang
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong, China
| | - Yunshan Guo
- Department of Statistics and Actuarial Science, The University of Hong Kong, Hong Kong, Hong Kong, China
| | - Jie V Zhao
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong, China
| | - Zhonghua Liu
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, New York, USA
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27
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Islam MM, Islam S, Ahmed R, Majumder M, Sarkar B, Himu MER, Kawser M, Hossain A, Mia MJ, Parag RR, Bulbul MRH, Ahmed S, Sattar MA, Biswas R, Das M, Rahman MM, Shil RK, Parial R, Chowdhury S, Das M, Noman ASM, Hossain MM. Reduced IFN-γ levels along with changes in hematologic and immunologic parameters are key to COVID-19 severity in Bangladeshi patients. Exp Hematol 2023; 118:53-64.e1. [PMID: 36574579 PMCID: PMC9701580 DOI: 10.1016/j.exphem.2022.11.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 11/08/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022]
Abstract
The manifestation of coronavirus disease 2019 (COVID-19) severity and mortality has been associated with dysregulation of the immune response, often influenced by racial disparities and conferred by changes in hematologic and immunologic parameters. These biological and hematologic parameters as well as cytokine profiles were investigated in a cohort of 61 COVID-19-positive patients (categorized into mild, moderate, and severe groups) from Bangladesh using standard analytical methods. The data reported that the interleukin (IL)-4 and IL-6 levels were significantly increased, whereas the levels of interferon (IFN)-γ were significantly reduced in patients with severe COVID-19 (p < 0.05) compared with those in patients with mild and/or moderate COVID-19. The extent of erythrocyte sedimentation rate (ESR); neutrophil count; and levels of ferritin, C-reactive protein (CRP), and D-dimer (p < 0.05) were found to be significantly increased, whereas the white blood cell (WBC), lymphocyte, eosinophil, and platelet counts (p < 0.05) were observed to be significantly reduced in patients with severe COVID-19 compared with those in the patients in other 2 groups. Our study exhibited a significantly higher IL-6-to-lymphocyte ratio in patients with severe COVID-19 than in those with mild and moderate COVID-19. The calculated neutrophil-to-lymphocyte ratio (NLR), platelet-to-lymphocyte ratio (PLR), lymphocyte-to-monocyte ratio (LMR), and ferritin-to-ESR ratio were significantly increased in patients with severe COVID-19. The increase in the IL-4 and IL-6 levels along with CRP and D-dimer levels may envisage a hyperinflammatory environment and immune dysregulation, which contribute to prolonged viral persistence, leading to severe disease. However, the reduced level of IFN-γ can be attributed to a less fatality toll in Bangladesh compared with that in the rest of the world.
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Affiliation(s)
- Mohammed Moinul Islam
- Department of Biochemistry & Molecular Biology, University of Chittagong, Chattogram, Bangladesh,EuGEF Research Foundation, Chattogram, Bangladesh
| | - Shafiqul Islam
- Department of Biochemistry & Molecular Biology, University of Chittagong, Chattogram, Bangladesh,EuGEF Research Foundation, Chattogram, Bangladesh,Stem Cell Genetics, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Ridwan Ahmed
- Department of Biochemistry & Molecular Biology, University of Chittagong, Chattogram, Bangladesh,EuGEF Research Foundation, Chattogram, Bangladesh
| | - Mohit Majumder
- Department of Biochemistry & Molecular Biology, University of Chittagong, Chattogram, Bangladesh,EuGEF Research Foundation, Chattogram, Bangladesh
| | - Bishu Sarkar
- Department of Biochemistry & Molecular Biology, University of Chittagong, Chattogram, Bangladesh,EuGEF Research Foundation, Chattogram, Bangladesh
| | - Md. Ejajur Rahman Himu
- Department of Biochemistry & Molecular Biology, University of Chittagong, Chattogram, Bangladesh,EuGEF Research Foundation, Chattogram, Bangladesh
| | - Md Kawser
- Department of Biochemistry & Molecular Biology, University of Chittagong, Chattogram, Bangladesh,EuGEF Research Foundation, Chattogram, Bangladesh
| | - Alamgir Hossain
- Department of Biochemistry & Molecular Biology, University of Chittagong, Chattogram, Bangladesh,EuGEF Research Foundation, Chattogram, Bangladesh
| | - Mohammad Jewel Mia
- Department of Biochemistry & Molecular Biology, University of Chittagong, Chattogram, Bangladesh,EuGEF Research Foundation, Chattogram, Bangladesh
| | - Rashed Rezwan Parag
- Department of Biochemistry & Molecular Biology, University of Chittagong, Chattogram, Bangladesh,EuGEF Research Foundation, Chattogram, Bangladesh
| | | | - Shakeel Ahmed
- Bangladesh Institute of Tropical and Infectious Diseases, Chattogram, Bangladesh
| | - MA Sattar
- Department of Medicine, Chittagong Medical College and Hospital, Chattogram, Bangladesh
| | - Rajdeep Biswas
- Anaesthesia & ICU department, General Hospital, Chattogram, Bangladesh
| | - Moumita Das
- Anaesthesia & ICU department, General Hospital, Chattogram, Bangladesh
| | - Md. Mizanur Rahman
- EuGEF Research Foundation, Chattogram, Bangladesh,Department of Biochemistry, Rangamati Medical College, Rangamati, Bangladesh
| | - Rajib Kumar Shil
- Department of Biochemistry & Molecular Biology, University of Chittagong, Chattogram, Bangladesh,EuGEF Research Foundation, Chattogram, Bangladesh
| | - Ramendu Parial
- Department of Biochemistry & Molecular Biology, University of Chittagong, Chattogram, Bangladesh,EuGEF Research Foundation, Chattogram, Bangladesh
| | - Srikanta Chowdhury
- Department of Biochemistry & Molecular Biology, University of Chittagong, Chattogram, Bangladesh,EuGEF Research Foundation, Chattogram, Bangladesh
| | - Manisha Das
- EuGEF Research Foundation, Chattogram, Bangladesh
| | - Abu Shadat Mohammod Noman
- Department of Biochemistry & Molecular Biology, University of Chittagong, Chattogram, Bangladesh,EuGEF Research Foundation, Chattogram, Bangladesh
| | - Muhammad Mosaraf Hossain
- Department of Biochemistry & Molecular Biology, University of Chittagong, Chattogram, Bangladesh; EuGEF Research Foundation, Chattogram, Bangladesh.
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28
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Ghazy AA, Alrasheedi AN, Elashri M, Moussa HH, Rashwan EK, Amer I, El Sharawy S, Elgamal S, Tawfik S, Abdelnasser M, Elsheredy A. Relevance of HLA-DP/DQ and INF-λ4 Polymorphisms to COVID-19 Outcomes. Br J Biomed Sci 2023; 80:11044. [PMID: 36743382 PMCID: PMC9894893 DOI: 10.3389/bjbs.2023.11044] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 01/11/2023] [Indexed: 01/22/2023]
Abstract
Background: Single nucleotide polymorphisms provide information on individuals' potential reactions to environmental factors, infections, diseases, as well as various therapies. A study on SNPs that influence SARS-CoV-2 susceptibility and severity may provide a predictive tool for COVID-19 outcomes and improve the customized coronavirus treatment. Aim: To evaluate the role of human leukocyte antigens DP/DQ and IFNλ4 polymorphisms on COVID-19 outcomes among Egyptian patients. Participants and Methods: The study involved 80 patients with severe COVID-19, 80 patients with mild COVID-19, and 80 non-infected healthy volunteers. Genotyping and allelic discrimination of HLA-DPrs3077 (G/A), HLA-DQrs7453920 (A/G), and IFNλ4 rs73555604 (C/T) SNPs were performed using real-time PCR. Results: Ages were 47.9 ± 8, 44.1 ± 12.1, and 45.8 ± 10 years in severe, mild and non-infected persons. There was a statistically significant association between severe COVID-19 and male gender (p = 0.002). A statistically significant increase in the frequency of HLA-DPrs3077G, HLA-DQrs7453920A, and IFNλ4rs73555604C alleles among severe COVID-19 patients when compared with other groups (p < 0.001). Coexistence of these alleles in the same individual increases the susceptibility to severe COVID-19 by many folds (p < 0.001). Univariate and multivariate logistic regression analysis for the studied parameters showed that old age, male gender, non-vaccination, HLA-DQ rs7453920AG+AA, HLA-DPrs3077GA+GG, and IFNλ4rs73555604CT+CC genotypes are independent risk factors for severe COVID-19 among Egyptian patients. Conclusion: HLA-DQ rs7453920A, HLA-DPrs3077G, and IFNλ4rs73555604C alleles could be used as markers of COVID-19 severity.
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Affiliation(s)
- Amany A. Ghazy
- Department of Pathology, Microbiology and Immunology Division, College of Medicine, Jouf University, Sakaka, Saudi Arabia,*Correspondence: Amany A. Ghazy,
| | - Abdullah N. Alrasheedi
- Department of Otolaryngology - Head and Neck Surgery, College of Medicine, Jouf University, Sakaka, Aljouf, Saudi Arabia
| | - Mohammed Elashri
- Department of Ophthalmology, Faculty of Medicine, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Hany Hussein Moussa
- Department of Chest Disease, Faculty of Medicine, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Eman K. Rashwan
- Department of Physiology, College of Medicine, Jouf University, Sakaka, Saudi Arabia
| | - Ibrahim Amer
- Department of Hepatology, Gastroenterology and Infectious Diseases, Faculty of Medicine, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Shimaa El Sharawy
- Department of Tropical Medicine and Infectious Diseases, Faculty of Medicine, Tanta University, Tanta, Egypt
| | - Shimaa Elgamal
- Department of Neurology, Faculty of Medicine, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Salwa Tawfik
- Department of Internal Medicine, National Research Center, Cairo, Egypt
| | | | - Amel Elsheredy
- Microbiology Department, Medical Research Institute, Alexandria University, Alexandria, Egypt
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29
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Shkurnikov M, Nersisyan S, Averinskaya D, Chekova M, Polyakov F, Titov A, Doroshenko D, Vechorko V, Tonevitsky A. HLA-A*01:01 allele diminishing in COVID-19 patients population associated with non-structural epitope abundance in CD8+ T-cell repertoire. PeerJ 2023; 11:e14707. [PMID: 36691482 PMCID: PMC9864130 DOI: 10.7717/peerj.14707] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 12/15/2022] [Indexed: 01/19/2023] Open
Abstract
In mid-2021, the SARS-CoV-2 Delta variant caused the third wave of the COVID-19 pandemic in several countries worldwide. The pivotal studies were aimed at studying changes in the efficiency of neutralizing antibodies to the spike protein. However, much less attention was paid to the T-cell response and the presentation of virus peptides by MHC-I molecules. In this study, we compared the features of the HLA-I genotype in symptomatic patients with COVID-19 in the first and third waves of the pandemic. As a result, we could identify the diminishing of carriers of the HLA-A*01:01 allele in the third wave and demonstrate the unique properties of this allele. Thus, HLA-A*01:01-binding immunoprevalent epitopes are mostly derived from ORF1ab. A set of epitopes from ORF1ab was tested, and their high immunogenicity was confirmed. Moreover, analysis of the results of single-cell phenotyping of T-cells in recovered patients showed that the predominant phenotype in HLA-A*01:01 carriers is central memory T-cells. The predominance of T-lymphocytes of this phenotype may contribute to forming long-term T-cell immunity in carriers of this allele. Our results can be the basis for highly effective vaccines based on ORF1ab peptides.
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Affiliation(s)
- Maxim Shkurnikov
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Stepan Nersisyan
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia,Institute of Molecular Biology, The National Academy of Sciences of the Republic of Armenia, Yerevan, Armenia,Armenian Bioinformatics Institute (ABI), Yerevan, Armenia,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Darya Averinskaya
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Milena Chekova
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Fedor Polyakov
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Aleksei Titov
- National Research Center for Hematology, Moscow, Russia
| | | | | | - Alexander Tonevitsky
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
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30
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Lake CM, Breen JJ. Sequence similarity between SARS-CoV-2 nucleocapsid and multiple sclerosis-associated proteins provides insight into viral neuropathogenesis following infection. Sci Rep 2023; 13:389. [PMID: 36617594 PMCID: PMC9825799 DOI: 10.1038/s41598-022-27348-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 12/30/2022] [Indexed: 01/09/2023] Open
Abstract
The novel coronavirus SARS-CoV-2 continues to cause death and disease throughout the world, underscoring the necessity of understanding the virus and host immune response. From the start of the pandemic, a prominent pattern of central nervous system (CNS) pathologies, including demyelination, has emerged, suggesting an underlying mechanism of viral mimicry to CNS proteins. We hypothesized that immunodominant epitopes of SARS-CoV-2 share homology with proteins associated with multiple sclerosis (MS). Using PEPMatch, a newly developed bioinformatics package which predicts peptide similarity within specific amino acid mismatching parameters consistent with published MHC binding capacity, we discovered that nucleocapsid protein shares significant overlap with 22 MS-associated proteins, including myelin proteolipid protein (PLP). Further computational evaluation demonstrated that this overlap may have critical implications for T cell responses in MS patients and is likely unique to SARS-CoV-2 among the major human coronaviruses. Our findings substantiate the hypothesis of viral molecular mimicry in the pathogenesis of MS and warrant further experimental exploration.
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Affiliation(s)
- Camille M. Lake
- grid.419681.30000 0001 2164 9667Office of Data Science and Emerging Technologies, National Institute of Allergy and Infectious Diseases, Rockville, MD USA
| | - Joseph J. Breen
- grid.419681.30000 0001 2164 9667Division of Allergy, Immunology and Transplantation, National Institute of Allergy and Infectious Diseases, Rockville, MD USA
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31
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Margaroli C, Benson P, Gastanadui MG, Song C, Viera L, Xing D, Wells JM, Patel R, Gaggar A, Payne GA. Spatial transcriptomic profiling of coronary endothelial cells in SARS-CoV-2 myocarditis. Front Med (Lausanne) 2023; 10:1118024. [PMID: 36968839 PMCID: PMC10034160 DOI: 10.3389/fmed.2023.1118024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 02/13/2023] [Indexed: 03/29/2023] Open
Abstract
Objectives Our objective was to examine coronary endothelial and myocardial programming in patients with severe COVID-19 utilizing digital spatial transcriptomics. Background Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has well-established links to thrombotic and cardiovascular events. Endothelial cell infection was initially proposed to initiate vascular events; however, this paradigm has sparked growing controversy. The significance of myocardial infection also remains unclear. Methods Autopsy-derived cardiac tissue from control (n = 4) and COVID-19 (n = 8) patients underwent spatial transcriptomic profiling to assess differential expression patterns in myocardial and coronary vascular tissue. Our approach enabled transcriptional profiling in situ with preserved anatomy and unaltered local SARS-CoV-2 expression. In so doing, we examined the paracrine effect of SARS-CoV-2 infection in cardiac tissue. Results We observed heterogeneous myocardial infection that tended to colocalize with CD31 positive cells within coronary capillaries. Despite these differences, COVID-19 patients displayed a uniform and unique myocardial transcriptional profile independent of local viral burden. Segmentation of tissues directly infected with SARS-CoV-2 showed unique, pro-inflammatory expression profiles including upregulated mediators of viral antigen presentation and immune regulation. Infected cell types appeared to primarily be capillary endothelial cells as differentially expressed genes included endothelial cell markers. However, there was limited differential expression within the endothelium of larger coronary vessels. Conclusion Our results highlight altered myocardial programming during severe COVID-19 that may in part be associated with capillary endothelial cells. However, similar patterns were not observed in larger vessels, diminishing endotheliitis, and endothelial activation as key drivers of cardiovascular events during COVID-19.
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Affiliation(s)
- Camilla Margaroli
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
- Program in Protease/Matrix Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Paul Benson
- Department of Pathology, Division of Anatomic Pathology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Maria G. Gastanadui
- Cardiopulmonary Research Program, University of Alabama at Birmingham, Birmingham, AL, United States
- Department of Medicine, Division of Cardiovascular Disease, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Chunyan Song
- Program in Protease/Matrix Biology, University of Alabama at Birmingham, Birmingham, AL, United States
- Cardiopulmonary Research Program, University of Alabama at Birmingham, Birmingham, AL, United States
- Department of Medicine, Division of Cardiovascular Disease, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Liliana Viera
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
- Program in Protease/Matrix Biology, University of Alabama at Birmingham, Birmingham, AL, United States
- Lung Health Center, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Dongqi Xing
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
- Program in Protease/Matrix Biology, University of Alabama at Birmingham, Birmingham, AL, United States
- Cardiopulmonary Research Program, University of Alabama at Birmingham, Birmingham, AL, United States
- Lung Health Center, University of Alabama at Birmingham, Birmingham, AL, United States
- Vascular Biology and Hypertension Program, University of Alabama at Birmingham, Birmingham, AL, United States
| | - J. Michael Wells
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
- Program in Protease/Matrix Biology, University of Alabama at Birmingham, Birmingham, AL, United States
- Cardiopulmonary Research Program, University of Alabama at Birmingham, Birmingham, AL, United States
- Lung Health Center, University of Alabama at Birmingham, Birmingham, AL, United States
- Vascular Biology and Hypertension Program, University of Alabama at Birmingham, Birmingham, AL, United States
- Medical Service at Birmingham VA Medical Center, Birmingham, AL, United States
| | - Rakesh Patel
- Program in Protease/Matrix Biology, University of Alabama at Birmingham, Birmingham, AL, United States
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL, United States
- Center for Free Radical Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Amit Gaggar
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
- Program in Protease/Matrix Biology, University of Alabama at Birmingham, Birmingham, AL, United States
- Cardiopulmonary Research Program, University of Alabama at Birmingham, Birmingham, AL, United States
- Lung Health Center, University of Alabama at Birmingham, Birmingham, AL, United States
- Vascular Biology and Hypertension Program, University of Alabama at Birmingham, Birmingham, AL, United States
- Medical Service at Birmingham VA Medical Center, Birmingham, AL, United States
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Gregory A. Payne
- Program in Protease/Matrix Biology, University of Alabama at Birmingham, Birmingham, AL, United States
- Cardiopulmonary Research Program, University of Alabama at Birmingham, Birmingham, AL, United States
- Department of Medicine, Division of Cardiovascular Disease, University of Alabama at Birmingham, Birmingham, AL, United States
- Vascular Biology and Hypertension Program, University of Alabama at Birmingham, Birmingham, AL, United States
- Medical Service at Birmingham VA Medical Center, Birmingham, AL, United States
- Comprehensive Cardiovascular Center, University of Alabama at Birmingham, Birmingham, AL, United States
- *Correspondence: Gregory A. Payne,
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32
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Lemieux W, Perreault J, Leiva-Torres GA, Baillargeon N, Yanez JC, Chevrier MC, Richard L, Lewin A, Trépanier P. HLA and red blood cell antigen genotyping in SARS-CoV-2 convalescent plasma donors. Future Virol 2023:10.2217/fvl-2022-0058. [PMID: 36844192 PMCID: PMC9941981 DOI: 10.2217/fvl-2022-0058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 01/11/2023] [Indexed: 02/22/2023]
Abstract
Aim: More data is required regarding the association between HLA allele and red blood cell (RBC) antigen expression in regard to SARS-CoV-2 infection and COVID-19 susceptibility. Methods: ABO, RhD, 37 other RBC antigens and HLA-A, B, C, DRB1, DQB1 and DPB1 were determined using high throughput platforms in 90 Caucasian convalescent plasma donors. Results: The AB group was significantly increased (1.5×, p = 0.018) and some HLA alleles were found to be significantly overrepresented (HLA-B*44:02, C*05:01, DPB1*04:01, DRB1*04:01 and DRB1*07:01) or underrepresented (A*01:01, B51:01 and DPB1*04:02) in convalescent individuals compared with the local bone marrow registry population. Conclusion: Our study of infection-susceptible but non-hospitalized Caucasian COVID-19 patients contributes to the global understanding of host genetic factors associated with SARS-CoV-2 infection and severity.
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Affiliation(s)
- William Lemieux
- 1Héma-Québec, Medical Affairs & Innovation, Québec City & Montréal, Québec, G1V 5G3, Canada
| | - Josée Perreault
- 1Héma-Québec, Medical Affairs & Innovation, Québec City & Montréal, Québec, G1V 5G3, Canada
| | | | - Nadia Baillargeon
- 2Héma-Québec, Transfusion Medicine, Québec City & Montréal, Québec, H4R 2W7, Canada
| | | | | | - Lucie Richard
- 2Héma-Québec, Transfusion Medicine, Québec City & Montréal, Québec, H4R 2W7, Canada
| | - Antoine Lewin
- 1Héma-Québec, Medical Affairs & Innovation, Québec City & Montréal, Québec, G1V 5G3, Canada
| | - Patrick Trépanier
- 1Héma-Québec, Medical Affairs & Innovation, Québec City & Montréal, Québec, G1V 5G3, Canada,Author for correspondence:
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Sei S, Ahadova A, Keskin DB, Bohaumilitzky L, Gebert J, von Knebel Doeberitz M, Lipkin SM, Kloor M. Lynch syndrome cancer vaccines: A roadmap for the development of precision immunoprevention strategies. Front Oncol 2023; 13:1147590. [PMID: 37035178 PMCID: PMC10073468 DOI: 10.3389/fonc.2023.1147590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 03/09/2023] [Indexed: 04/11/2023] Open
Abstract
Hereditary cancer syndromes (HCS) account for 5~10% of all cancer diagnosis. Lynch syndrome (LS) is one of the most common HCS, caused by germline mutations in the DNA mismatch repair (MMR) genes. Even with prospective cancer surveillance, LS is associated with up to 50% lifetime risk of colorectal, endometrial, and other cancers. While significant progress has been made in the timely identification of germline pathogenic variant carriers and monitoring and early detection of precancerous lesions, cancer-risk reduction strategies are still centered around endoscopic or surgical removal of neoplastic lesions and susceptible organs. Safe and effective cancer prevention strategies are critically needed to improve the life quality and longevity of LS and other HCS carriers. The era of precision oncology driven by recent technological advances in tumor molecular profiling and a better understanding of genetic risk factors has transformed cancer prevention approaches for at-risk individuals, including LS carriers. MMR deficiency leads to the accumulation of insertion and deletion mutations in microsatellites (MS), which are particularly prone to DNA polymerase slippage during DNA replication. Mutations in coding MS give rise to frameshift peptides (FSP) that are recognized by the immune system as neoantigens. Due to clonal evolution, LS tumors share a set of recurrent and predictable FSP neoantigens in the same and in different LS patients. Cancer vaccines composed of commonly recurring FSP neoantigens selected through prediction algorithms have been clinically evaluated in LS carriers and proven safe and immunogenic. Preclinically analogous FSP vaccines have been shown to elicit FSP-directed immune responses and exert tumor-preventive efficacy in murine models of LS. While the immunopreventive efficacy of "off-the-shelf" vaccines consisting of commonly recurring FSP antigens is currently investigated in LS clinical trials, the feasibility and utility of personalized FSP vaccines with individual HLA-restricted epitopes are being explored for more precise targeting. Here, we discuss recent advances in precision cancer immunoprevention approaches, emerging enabling technologies, research gaps, and implementation barriers toward clinical translation of risk-tailored prevention strategies for LS carriers. We will also discuss the feasibility and practicality of next-generation cancer vaccines that are based on personalized immunogenic epitopes for precision cancer immunoprevention.
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Affiliation(s)
- Shizuko Sei
- Division of Cancer Prevention, National Cancer Institute, National Institutes of Health, Rockville, MD, United States
- *Correspondence: Shizuko Sei, ; Steven M. Lipkin, ; Matthias Kloor,
| | - Aysel Ahadova
- Department of Applied Tumor Biology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Center Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Derin B. Keskin
- Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, MA, United States
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
- Broad Institute of The Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, United States
- Department of Computer Science, Metropolitan College, Boston University, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Lena Bohaumilitzky
- Department of Applied Tumor Biology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Center Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Johannes Gebert
- Department of Applied Tumor Biology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Center Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Magnus von Knebel Doeberitz
- Department of Applied Tumor Biology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Center Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Steven M. Lipkin
- Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medical College, New York, NY, United States
- *Correspondence: Shizuko Sei, ; Steven M. Lipkin, ; Matthias Kloor,
| | - Matthias Kloor
- Department of Applied Tumor Biology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Center Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
- *Correspondence: Shizuko Sei, ; Steven M. Lipkin, ; Matthias Kloor,
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Amirian P, Zarpoosh M, Moradi S, Jalili C. Celiac disease and COVID-19 in adults: A systematic review. PLoS One 2023; 18:e0285880. [PMID: 37192180 DOI: 10.1371/journal.pone.0285880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 05/03/2023] [Indexed: 05/18/2023] Open
Abstract
BACKGROUND Celiac disease (CD) is an autoimmune disease affecting around 1.4% of the total human population. Local and systemic manifestations are described in CD. Viral infections seem to trigger CD or even have a worse outcome in CD patients. The evidence on the relationship between CD and coronavirus disease (COVID-19) is limited. To evaluate existing evidence on the association between CD and COVID-19, we conducted the current systematic review. METHODS We systematically searched Pubmed, Scopus, and Embase databases to find articles that reported risks or outcomes of COVID-19 in CD patients. Papers in any language published up to November 17, 2022, were evaluated for possible inclusion. The results were analyzed qualitatively. This study is registered with PROSPERO(CRD42022327380). RESULTS We identified 509 studies by searching databases; 14 reported data on the risk or outcome of COVID-19 in CD patients and were eligible for qualitative synthesis. We found that the relative risk of acquiring COVID-19 in CD patients may be lower than in the general population. Approximately 90% of infected patients were treated as an outpatient, and 10% were hospitalized. GFD adherence and Health-related quality of life (HR-QOL) were more or less the same before and during the pandemic. The gluten-free products (GFP) supply seems to be plunged during the pandemic. The data on the psychological effects of the pandemic were conflicting. CONCLUSION The risk of acquiring COVID-19 in CD patients is lower than in the general population. Females were more likely to be infected by COVID-19, and the most common comorbidity in infected patients was a chronic lower respiratory disease; around 10% of infected patients needed hospitalization, GFD adherence, and HR-QOL was more or less the same before and during the pandemic, depression, anxiety, and stress levels of patients varied among studies. Patients had more difficulties accessing GFPs based on limited data.
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Affiliation(s)
- Parsa Amirian
- General Practitioner, Kermanshah University of Medical Science (KUMS), Kermanshah, Iran
| | - Mahsa Zarpoosh
- General Practitioner, Kermanshah University of Medical Science (KUMS), Kermanshah, Iran
| | - Sajjad Moradi
- Nutritional Sciences Department, School of Nutritional Sciences and Food Technology, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Cyrus Jalili
- Medical Biology Research Centre, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
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Arab F, Mollazadeh S, Ghayourbabaei F, Moghbeli M, Saburi E. The role of HLA genotypes in understanding the pathogenesis of severe COVID-19. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2023; 24:14. [PMID: 36718139 PMCID: PMC9878497 DOI: 10.1186/s43042-023-00392-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 01/18/2023] [Indexed: 01/27/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has caused human tragedy through the global spread of the viral pathogen SARS-CoV-2. Although the underlying factors for the severity of COVID-19 in different people are still unknown, several gene variants can be used as predictors of disease severity, particularly variations in viral receptor genes such as angiotensin-converting enzyme 2 (ACE2) or major histocompatibility complex (MHC) genes. The reaction of the immune system, as the most important defense strategy in the case of viruses, plays a decisive role. The innate immune system is important both as a primary line of defense and as a trigger of the acquired immune response. The HLA-mediated acquired immune response is linked to the acquired immune system. In various diseases, it has been shown that genetic alterations in components of the immune system can play a crucial role in how the body responds to pathogens, especially viruses. One of the most important host genetic factors is the human leukocyte antigen (HLA) profile, which includes HLA classes I and II and may be symbolic of the diversity of immune response and genetic predisposition in disease progression. COVID-19 will have direct contact with the acquired immune system as an intracellular pathogen after exposure to the proteasome and its components through class I HLA. Therefore, it is assumed that in different genotypes of the HLA-I class, an undesirable supply causes an insufficient activation of the immune system. Insufficient binding of antigen delivered by class I HLA to host lymphocytes results in uncertain identification and insufficient activation of the acquired immune system. The absence of secretion of immune cytokines such as interferons, which play an important role in controlling viral infection in the early stages, is a complication of this event. Understanding the allelic diversity of HLA in people infected with coronavirus compared with uninfected people of one race not only allows identification of people with HLA susceptible to COVID-19 but also provides better insight into the behavior of the virus, which helps to take effective preventive and curative measures earlier.
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Affiliation(s)
- Fatemeh Arab
- grid.411583.a0000 0001 2198 6209Medical Genetics and Molecular Medicine Department, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Samaneh Mollazadeh
- grid.464653.60000 0004 0459 3173Natural Products and Medicinal Plants Research Center, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Farnaz Ghayourbabaei
- grid.411301.60000 0001 0666 1211Department of Biology, Faculty of Sciences, University of Ferdowsi, Mashhad, Iran
| | - Meysam Moghbeli
- grid.411583.a0000 0001 2198 6209Medical Genetics and Molecular Medicine Department, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Ehsan Saburi
- grid.411583.a0000 0001 2198 6209Medical Genetics and Molecular Medicine Department, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
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Immunogenetic Predisposition to SARS-CoV-2 Infection. BIOLOGY 2022; 12:biology12010037. [PMID: 36671730 PMCID: PMC9855425 DOI: 10.3390/biology12010037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/15/2022] [Accepted: 12/20/2022] [Indexed: 12/28/2022]
Abstract
Herein, we included 527 individuals from two Hospitals, Chemnitz and University-Hospital Leipzig. In total, 199 were negative for PCR and 328 were positive upon first admission. We used next generation sequencing for HLA-A, B, C, DRB1, DRB345, DQA1, DQB1, DPA1, and DPB1, and in some cases, HLA-E, F, G, and H. Furthermore, we molecularly defined 22 blood group systems comprising 26 genes and 5 platelet antigen genes. We observed a significant enrichment of homozygosity for DQA/DQB in the positive group. Within the negative subjects, HLA-B*57:01, HLA-B*55:01, DRB1*13:01, and DRB1*01:01 were enriched, and in the positive group, homozygosity for DQA/DQB, DRB1*09:01, and DRB1*15:01 was observed. DQA1*01:01, DQA1*02:01, and DQA1*01:03 were enriched in the negative group. HLA-DQB1*06:02 was enriched in the positive group, and HLA-DQB1*05:01 and HLA-DQB1*06:03 were enriched in the negative group. For the blood group systems MNS, RH, LE, FY, JK, YT, DO, and KN, enrichment was seen in both groups, depending on the antigen under observation. Homozygosity for D-positive RHD alleles, as well as the phenotypes M-N+ of the MNS blood group system and Yk(a-) of the KN system, were enriched in the positive group. All of these significances disappeared upon correction. Subjects who carried homozygous HPA-1a were more frequent in the negative group, contrasting with the finding that HPA-1ab was enriched in the positive group.
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Abstract
BACKGROUND The coronavirus disease 2019 (COVID-19), an acute respiratory disease caused by a novel coronavirus (SARS-CoV-2), is emerging as a worldwide public health emergency. Several scientific contributions reported the potential relevance of human leukocyte antigen (HLA) polymorphism and susceptibility to viruses, such as SARS-CoV. In our study, we examined a population of coeliac subjects presenting the HLA haplotype DQ2 and/or DQ8. Our aim was to evaluate whether HLA DQ2 and/or DQ8 haplotype play a role in SARS-CoV-2-infection. The aim was also to evaluate the difficulty in following the gluten-free diet due to all the adversities produced by the pandemic, such as the food supply disruption, and the difficulties in managing the clinical follow-up. METHODS 191 consecutive coeliac patients completed a questionnaire on their current clinical status, psychological effects, and management of the gluten-free diet experienced during the COVID-19 pandemic and questions regarding possible SARS-CoV-2 infection. RESULTS Out of the 191 patients who participated in the study, 42 were full-blown coeliac and 149 were in remission. From the answers provided, 84.8% of patients declared that they no longer consider themselves vulnerable to COVID-19 as they suffer from coeliac disease; 94.2% of patients did not encounter any difficulties in managing the gluten-free diet or in acquiring specific foods and 64.9% of patients in our study underwent diagnostic testing for SARS-CoV-2. Out of this number, 31.5% did so due to contacts with subjects affected by COVID-19, 26.6% for work related reasons, 11.3% due to flu-like symptoms and 30.6% for other reasons. Only 5.8% of the enrolled patients received a diagnosis of COVID-19. Out of all the patients in our population who were diagnosed with COVID-19, 94.8% developed no symptoms and none of them needed hospitalization or intensive care. CONCLUSION The hypothesis that the HLADQ2 and/or DQ8 haplotype plays a protective role against SARS-CoV-2 infection, as against other viral infections, is intriguingly suggestive.KEY MESSAGESCOVID-19 as a public health emergency;SARS-CoV-2 and possible complications in coeliac disease;Role of HLA DQ2 and/or DQ8 in SARS-CoV-2 infection.
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Affiliation(s)
- N Greco
- Department of Translational and Precision Medicine, Sapienza University of Rome, Rome, Italy
| | - A Meacci
- Department of Translational and Precision Medicine, Sapienza University of Rome, Rome, Italy
| | - B Mora
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - A Vestri
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Rome, Italy
| | - A Picarelli
- Department of Translational and Precision Medicine, Sapienza University of Rome, Rome, Italy
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Abstract
BACKGROUND The coronavirus disease 2019 (COVID-19), an acute respiratory disease caused by a novel coronavirus (SARS-CoV-2), is emerging as a worldwide public health emergency. Several scientific contributions reported the potential relevance of human leukocyte antigen (HLA) polymorphism and susceptibility to viruses, such as SARS-CoV. In our study, we examined a population of coeliac subjects presenting the HLA haplotype DQ2 and/or DQ8. Our aim was to evaluate whether HLA DQ2 and/or DQ8 haplotype play a role in SARS-CoV-2-infection. The aim was also to evaluate the difficulty in following the gluten-free diet due to all the adversities produced by the pandemic, such as the food supply disruption, and the difficulties in managing the clinical follow-up. METHODS 191 consecutive coeliac patients completed a questionnaire on their current clinical status, psychological effects, and management of the gluten-free diet experienced during the COVID-19 pandemic and questions regarding possible SARS-CoV-2 infection. RESULTS Out of the 191 patients who participated in the study, 42 were full-blown coeliac and 149 were in remission. From the answers provided, 84.8% of patients declared that they no longer consider themselves vulnerable to COVID-19 as they suffer from coeliac disease; 94.2% of patients did not encounter any difficulties in managing the gluten-free diet or in acquiring specific foods and 64.9% of patients in our study underwent diagnostic testing for SARS-CoV-2. Out of this number, 31.5% did so due to contacts with subjects affected by COVID-19, 26.6% for work related reasons, 11.3% due to flu-like symptoms and 30.6% for other reasons. Only 5.8% of the enrolled patients received a diagnosis of COVID-19. Out of all the patients in our population who were diagnosed with COVID-19, 94.8% developed no symptoms and none of them needed hospitalization or intensive care. CONCLUSION The hypothesis that the HLADQ2 and/or DQ8 haplotype plays a protective role against SARS-CoV-2 infection, as against other viral infections, is intriguingly suggestive.KEY MESSAGESCOVID-19 as a public health emergency;SARS-CoV-2 and possible complications in coeliac disease;Role of HLA DQ2 and/or DQ8 in SARS-CoV-2 infection.
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Affiliation(s)
- N Greco
- Department of Translational and Precision Medicine, Sapienza University of Rome, Rome, Italy
| | - A Meacci
- Department of Translational and Precision Medicine, Sapienza University of Rome, Rome, Italy
| | - B Mora
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - A Vestri
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Rome, Italy
| | - A Picarelli
- Department of Translational and Precision Medicine, Sapienza University of Rome, Rome, Italy
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Chen LC, Nersisyan S, Wu CJ, Chang CM, Tonevitsky A, Guo CL, Chang WC. On the peptide binding affinity changes in population-specific HLA repertoires to the SARS-CoV-2 variants Delta and Omicron. J Autoimmun 2022; 133:102952. [PMID: 36427410 PMCID: PMC9650568 DOI: 10.1016/j.jaut.2022.102952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 11/05/2022] [Accepted: 11/06/2022] [Indexed: 11/13/2022]
Abstract
OBJECTIVE To investigate the changes of Spike protein-HLA binding affinity profiles between the Wuhan strain and two dominant variants, the Delta and the Omicron strains, among the Taiwanese, the British and the Russian populations. METHODS The HLA frequencies and the HLA-peptide binding affinity profiles in the T-CoV database were combined to conduct the study. We focused on the public alleles in the three populations (HLA-A, HLA-B, HLA-C, HLA-DRB1, and/or HLA-DPA1/DPB1 alleles) and the altered peptides of the spike protein (compared to the Wuhan strain) in the Delta G/478K·V1 (B.1.617.2 + AY.1 + AY.2) and the Omicron (BA.1) strains. RESULTS For the Delta strain, tight bindings of the altered peptides to the HLA alleles decrease in all three populations and almost vanish in the Taiwanese population. For the Omicron strain, tight bindings are mostly preserved for both HLA classes and in the Taiwanese and the British populations, with a slight reduction in HLA class II in the Taiwanese (1.4%), while the Russian population preserves a relatively high fraction of tight bindings for both HLA classes. CONCLUSION We comprehensively reported the changes in the HLA-associated SARS-CoV-2 Spike protein peptide binding profiles among the Taiwanese, the British, and the Russian populations. Further studies are needed to understand the immunological mechanisms and the clinical value of our findings.
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Affiliation(s)
- Lu-Chun Chen
- Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Stepan Nersisyan
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia,Institute of Molecular Biology, The National Academy of Sciences of the Republic of Armenia, Yerevan, Armenia,Armenian Bioinformatics Institute (ABI), Yerevan, Armenia
| | - Chang-Jiun Wu
- Department of Genomic Medicine, University of Texas, MD Anderson Cancer Center. Houston Texas, USA
| | - Che-Mai Chang
- Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Alexander Tonevitsky
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Chin-Lin Guo
- Institute of Physics, Academia Sinica, Taipei, Taiwan,Corresponding author. Institute of Physics, Academia Sinica, No. 128, Sec. 2, Academia Rd., Nangang Dist., Taipei City 115201, Taiwan. Tel.: (886) 988545414
| | - Wei-Chiao Chang
- Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, Taipei, Taiwan,Department of Medical Education and Research, Integrative Research Center for Critical Care, Wan fang Hospital, Taipei Medical University, Taipei, Taiwan,Master Program in Clinical Genomics and Proteomics, School of Pharmacy, Taipei Medical University, Taipei, Taiwan,Department of Pharmacy, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan,Corresponding author. Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, No. 250 Wuxing St., Xinyi Dist., Taipei City 110, Taiwan. Tel.: (886) 928121979
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Lu X, Yamasaki S. Current understanding of T cell immunity against SARS-CoV-2. Inflamm Regen 2022; 42:51. [PMID: 36447270 PMCID: PMC9706904 DOI: 10.1186/s41232-022-00242-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 11/17/2022] [Indexed: 11/30/2022] Open
Abstract
As an important part of adaptive immunity, T cells are indispensable in the defense against pathogens including viruses. SARS-CoV-2 is a new human coronavirus that occurred at the end of 2019 and has caused the COVID-19 pandemic. Nevertheless, most of the infected patients recovered without any antiviral therapies, suggesting an effective immunity developed in the bodies. T cell immunity responds upon SARS-CoV-2 infection or vaccination and plays crucial roles in eliminating the viruses and generating T cell memory. Specifically, a subpopulation of CD4+ T cells could support the production of anti-SARS-CoV-2 antibodies, and cytotoxic CD8+ T cells are also protective against the infection. SARS-CoV-2-recognizing T cells could be detected in SARS-CoV-2-unexposed donors, but the role of these cross-reactive T cells is still in debate. T cell responses could be diverse across individuals, mainly due to the polymorphism of HLAs. Thus, compared to antibodies, T cell responses are generally less affected by the mutations of SARS-CoV-2 variants. Up to now, a huge number of studies on SARS-CoV-2-responsive T cells have been published. In this review, we introduced some major findings addressing the questions in the main aspects about T cell responses elicited by SARS-CoV-2, to summarize the current understanding of COVID-19.
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Affiliation(s)
- Xiuyuan Lu
- grid.136593.b0000 0004 0373 3971Laboratory of Molecular Immunology, Immunology Frontier Research Center, Osaka University, Suita, 565-0871 Japan ,grid.136593.b0000 0004 0373 3971Epitope Analysis Team, Center for Advanced Modalities and DDS, Osaka University, Suita, 565-0871 Japan
| | - Sho Yamasaki
- grid.136593.b0000 0004 0373 3971Laboratory of Molecular Immunology, Immunology Frontier Research Center, Osaka University, Suita, 565-0871 Japan ,grid.136593.b0000 0004 0373 3971Epitope Analysis Team, Center for Advanced Modalities and DDS, Osaka University, Suita, 565-0871 Japan ,grid.136593.b0000 0004 0373 3971Department of Molecular Immunology, Research Institute for Microbial Diseases, Osaka University, Suita, 565-0871 Japan ,grid.136593.b0000 0004 0373 3971Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, 565-0871 Japan ,grid.177174.30000 0001 2242 4849Division of Molecular Design, Research Center for Systems Immunology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582 Japan
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Park JS, Kim K. Antigen Coverage Presented by MHC Class I Has a Negative Correlation with SARS-CoV-2-Induced Mortality. Vaccines (Basel) 2022; 10:1917. [PMID: 36423013 PMCID: PMC9698063 DOI: 10.3390/vaccines10111917] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/29/2022] [Accepted: 11/09/2022] [Indexed: 11/11/2023] Open
Abstract
The COVID-19 pandemic has caused a health crisis worldwide; therefore, it is necessary to understand the factors related to its prognosis. In this study, we hypothesized that SARS-CoV-2-derived antigens presented by MHC class I may correlate with mortality in COVID-19 because they induce adaptive immune responses. Antigen coverage at the national level was inferred using country-specific HLA allele frequencies and relative predictions of binding antigens. We performed regression analysis between antigen coverage and the death rate due to COVID-19 across countries and found a negative correlation, although it was statistically significant only in HLA-B. This negative correlation was corroborated in multiple regression analysis with known risk factors, such as the prevalence of underlying disease. Furthermore, we analyzed antigen coverage in accordance with SARS-CoV-2 domains and identified a significant negative correlation when it was derived from the spike domain, which is reported to be favorable for COVID-19 prognosis. Taken together, the results indicate that the antigen coverage of SARS-CoV-2 specifically presented by HLA-B may act as a favorable factor when explaining COVID-19-induced mortality.
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Affiliation(s)
- Ji Soo Park
- Department of Biology, Kyung Hee University, Seoul 02447, Korea
| | - Kwoneel Kim
- Department of Biology, Kyung Hee University, Seoul 02447, Korea
- Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul 02447, Korea
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Bubnova L, Pavlova I, Terentieva M, Glazanova T, Belyaeva E, Sidorkevich S, Bashketova N, Chkhingeria I, Kozhemyakina M, Azarov D, Kuznetsova R, Ramsay ES, Gladkikh A, Sharova A, Dedkov V, Totolian A. HLA Genotypes in Patients with Infection Caused by Different Strains of SARS-CoV-2. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:14024. [PMID: 36360904 PMCID: PMC9657774 DOI: 10.3390/ijerph192114024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 10/21/2022] [Accepted: 10/24/2022] [Indexed: 06/16/2023]
Abstract
The aggressive infectious nature of SARS-CoV-2, its rapid spread, and the emergence of mutations necessitate investigation of factors contributing to differences in SARS-CoV-2 susceptibility and severity. The role of genetic variations in the human HLA continues to be studied in various populations in terms of both its effect on morbidity and clinical manifestation of illness. The study included 484 COVID-19 convalescents (northwest Russia residents of St. Petersburg). Cases in which the responsible strain was determined were divided in two subgroups: group 1 (n = 231) had illness caused by genovariants unrelated to variant of concern (VOC) strains; and group 2 (n = 80) had illness caused by the delta (B.1.617.2) VOC; and a control group (n = 1456). DNA typing (HLA-A, B, DRB1) was performed at the basic resolution level. HLA-A*02 was associated with protection against infection caused by non-VOC SARS-CoV-2 genetic variants only but not against infection caused by delta strains. HLA-A*03 was associated with protection against infection caused by delta strains; and allele groups associated with infection by delta strains were HLA-A*30, B*49, and B*57. Thus, in northwest Russia, HLA-A*02 was associated with protection against infection caused by non-VOC SARS-CoV-2 genetic variants but not against delta viral strains. HLA-A*03 was associated with a reduced risk of infection by delta SARS-CoV-2 strains. HLA-A*30, HLA-B*49, and HLA-B*57 allele groups were predisposing factors for infection by delta (B.1.617.2) strains.
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Affiliation(s)
- Ludmila Bubnova
- Russian Research Institute of Hematology and Transfusion Science, FMBA, 191024 St. Petersburg, Russia
- Department of immunology, Faculty of medicine, Pavlov First Saint Petersburg State Medical University, Russian Ministry of Health, 197022 St. Petersburg, Russia
| | - Irina Pavlova
- Russian Research Institute of Hematology and Transfusion Science, FMBA, 191024 St. Petersburg, Russia
| | - Maria Terentieva
- Russian Research Institute of Hematology and Transfusion Science, FMBA, 191024 St. Petersburg, Russia
| | - Tatiana Glazanova
- Russian Research Institute of Hematology and Transfusion Science, FMBA, 191024 St. Petersburg, Russia
| | - Elena Belyaeva
- Russian Research Institute of Hematology and Transfusion Science, FMBA, 191024 St. Petersburg, Russia
| | - Sergei Sidorkevich
- Russian Research Institute of Hematology and Transfusion Science, FMBA, 191024 St. Petersburg, Russia
| | - Nataliya Bashketova
- Saint Petersburg Office, Federal Service for Consumer Rights Protection and Human Welfare, 191025 St. Petersburg, Russia
| | - Irina Chkhingeria
- Saint Petersburg Office, Federal Service for Consumer Rights Protection and Human Welfare, 191025 St. Petersburg, Russia
| | | | - Daniil Azarov
- Saint Petersburg Center for Hygiene and Epidemiology, 191023 St. Petersburg, Russia
| | - Raisa Kuznetsova
- Department of immunology, Faculty of medicine, Pavlov First Saint Petersburg State Medical University, Russian Ministry of Health, 197022 St. Petersburg, Russia
- Saint Petersburg Pasteur Research Institute of Epidemiology and Microbiology, 197101 St. Petersburg, Russia
| | - Edward S. Ramsay
- Saint Petersburg Pasteur Research Institute of Epidemiology and Microbiology, 197101 St. Petersburg, Russia
| | - Anna Gladkikh
- Saint Petersburg Pasteur Research Institute of Epidemiology and Microbiology, 197101 St. Petersburg, Russia
| | - Alena Sharova
- Saint Petersburg Pasteur Research Institute of Epidemiology and Microbiology, 197101 St. Petersburg, Russia
| | - Vladimir Dedkov
- Saint Petersburg Pasteur Research Institute of Epidemiology and Microbiology, 197101 St. Petersburg, Russia
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University, 119435 Moscow, Russia
| | - Areg Totolian
- Department of immunology, Faculty of medicine, Pavlov First Saint Petersburg State Medical University, Russian Ministry of Health, 197022 St. Petersburg, Russia
- Saint Petersburg Pasteur Research Institute of Epidemiology and Microbiology, 197101 St. Petersburg, Russia
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Castelli EC, de Castro MV, Naslavsky MS, Scliar MO, Silva NSB, Pereira RN, Ciriaco VAO, Castro CFB, Mendes-Junior CT, Silveira EDS, de Oliveira IM, Antonio EC, Vieira GF, Meyer D, Nunes K, Matos LRB, Silva MVR, Wang JYT, Esposito J, Cória VR, Magawa JY, Santos KS, Cunha-Neto E, Kalil J, Bortolin RH, Hirata MH, Dell’Aquila LP, Razuk-Filho A, Batista-Júnior PB, Duarte-Neto AN, Dolhnikoff M, Saldiva PHN, Passos-Bueno MR, Zatz M. MUC22, HLA-A, and HLA-DOB variants and COVID-19 in resilient super-agers from Brazil. Front Immunol 2022; 13:975918. [PMID: 36389712 PMCID: PMC9641602 DOI: 10.3389/fimmu.2022.975918] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 09/15/2022] [Indexed: 08/08/2023] Open
Abstract
BACKGROUND Although aging correlates with a worse prognosis for Covid-19, super elderly still unvaccinated individuals presenting mild or no symptoms have been reported worldwide. Most of the reported genetic variants responsible for increased disease susceptibility are associated with immune response, involving type I IFN immunity and modulation; HLA cluster genes; inflammasome activation; genes of interleukins; and chemokines receptors. On the other hand, little is known about the resistance mechanisms against SARS-CoV-2 infection. Here, we addressed polymorphisms in the MHC region associated with Covid-19 outcome in super elderly resilient patients as compared to younger patients with a severe outcome. METHODS SARS-CoV-2 infection was confirmed by RT-PCR test. Aiming to identify candidate genes associated with host resistance, we investigated 87 individuals older than 90 years who recovered from Covid-19 with mild symptoms or who remained asymptomatic following positive test for SARS-CoV-2 as compared to 55 individuals younger than 60 years who had a severe disease or died due to Covid-19, as well as to the general elderly population from the same city. Whole-exome sequencing and an in-depth analysis of the MHC region was performed. All samples were collected in early 2020 and before the local vaccination programs started. RESULTS We found that the resilient super elderly group displayed a higher frequency of some missense variants in the MUC22 gene (a member of the mucins' family) as one of the strongest signals in the MHC region as compared to the severe Covid-19 group and the general elderly control population. For example, the missense variant rs62399430 at MUC22 is two times more frequent among the resilient super elderly (p = 0.00002, OR = 2.24). CONCLUSION Since the pro-inflammatory basal state in the elderly may enhance the susceptibility to severe Covid-19, we hypothesized that MUC22 might play an important protective role against severe Covid-19, by reducing overactive immune responses in the senior population.
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Affiliation(s)
- Erick C. Castelli
- Department of Pathology, School of Medicine, São Paulo State University (UNESP), Botucatu, Brazil
- Molecular Genetics and Bioinformatics Laboratory, Experimental Research Unit (Unipex), School of Medicine, São Paulo State University (UNESP), Botucatu, Brazil
| | - Mateus V. de Castro
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - Michel S. Naslavsky
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, Brazil
| | - Marilia O. Scliar
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - Nayane S. B. Silva
- Molecular Genetics and Bioinformatics Laboratory, Experimental Research Unit (Unipex), School of Medicine, São Paulo State University (UNESP), Botucatu, Brazil
| | - Raphaela N. Pereira
- Molecular Genetics and Bioinformatics Laboratory, Experimental Research Unit (Unipex), School of Medicine, São Paulo State University (UNESP), Botucatu, Brazil
| | - Viviane A. O. Ciriaco
- Molecular Genetics and Bioinformatics Laboratory, Experimental Research Unit (Unipex), School of Medicine, São Paulo State University (UNESP), Botucatu, Brazil
| | - Camila F. B. Castro
- Molecular Genetics and Bioinformatics Laboratory, Experimental Research Unit (Unipex), School of Medicine, São Paulo State University (UNESP), Botucatu, Brazil
- Centro Universitário Sudoeste Paulista, Avaré, Brazil
| | - Celso T. Mendes-Junior
- Departamento de Química, Faculdade de Filosofa, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Etiele de S. Silveira
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Iuri M. de Oliveira
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Eduardo C. Antonio
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Gustavo F. Vieira
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
- Laboratório de Saúde Humana In Silico, Programa de Pós-Graduação em Saúde e Desenvolvimento Humano, Universidade La Salle, Canoas, Brazil
| | - Diogo Meyer
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, Brazil
| | - Kelly Nunes
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, Brazil
| | - Larissa R. B. Matos
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - Monize V. R. Silva
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - Jaqueline Y. T. Wang
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - Joyce Esposito
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - Vivian R. Cória
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - Jhosiene Y. Magawa
- Departamento de Clínica Médica, Disciplina de Alergia e Imunologia Clínica, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Laboratório de Imunologia, Instituto do Coração (InCor), LIM19, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, Brazil
- Instituto de Investigação em Imunologia, Instituto Nacional de Ciências e Tecnologia-iii (INCT), São Paulo, Brazil
| | - Keity S. Santos
- Departamento de Clínica Médica, Disciplina de Alergia e Imunologia Clínica, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Laboratório de Imunologia, Instituto do Coração (InCor), LIM19, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, Brazil
- Instituto de Investigação em Imunologia, Instituto Nacional de Ciências e Tecnologia-iii (INCT), São Paulo, Brazil
| | - Edecio Cunha-Neto
- Departamento de Clínica Médica, Disciplina de Alergia e Imunologia Clínica, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Laboratório de Imunologia, Instituto do Coração (InCor), LIM19, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, Brazil
- Instituto de Investigação em Imunologia, Instituto Nacional de Ciências e Tecnologia-iii (INCT), São Paulo, Brazil
| | - Jorge Kalil
- Departamento de Clínica Médica, Disciplina de Alergia e Imunologia Clínica, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Laboratório de Imunologia, Instituto do Coração (InCor), LIM19, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, Brazil
- Instituto de Investigação em Imunologia, Instituto Nacional de Ciências e Tecnologia-iii (INCT), São Paulo, Brazil
| | - Raul H. Bortolin
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Mário Hiroyuki Hirata
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | | | | | | | - Amaro N. Duarte-Neto
- Department of Pathology, School of Medicine, University of Sao Paulo, Sao Paulo, Brazil
| | - Marisa Dolhnikoff
- Department of Pathology, School of Medicine, University of Sao Paulo, Sao Paulo, Brazil
| | - Paulo H. N. Saldiva
- Department of Pathology, School of Medicine, University of Sao Paulo, Sao Paulo, Brazil
| | - Maria Rita Passos-Bueno
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, Brazil
| | - Mayana Zatz
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, Brazil
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Gustiananda M, Julietta V, Hermawan A, Febriana GG, Hermantara R, Kristiani L, Sidhartha E, Sutejo R, Agustriawan D, Andarini S, Parikesit AA. Immunoinformatics Identification of the Conserved and Cross-Reactive T-Cell Epitopes of SARS-CoV-2 with Human Common Cold Coronaviruses, SARS-CoV, MERS-CoV and Live Attenuated Vaccines Presented by HLA Alleles of Indonesian Population. Viruses 2022; 14:v14112328. [PMID: 36366426 PMCID: PMC9699331 DOI: 10.3390/v14112328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/13/2022] [Accepted: 10/16/2022] [Indexed: 02/01/2023] Open
Abstract
Reports on T-cell cross-reactivity against SARS-CoV-2 epitopes in unexposed individuals have been linked with prior exposure to the human common cold coronaviruses (HCCCs). Several studies suggested that cross-reactive T-cells response to live attenuated vaccines (LAVs) such as BCG (Bacillus Calmette-Guérin), OPV (Oral Polio Vaccine), and MMR (measles, mumps, and rubella) can limit the development and severity of COVID-19. This study aims to identify potential cross-reactivity between SARS-CoV-2, HCCCs, and LAVs in the context of T-cell epitopes peptides presented by HLA (Human Leukocyte Antigen) alleles of the Indonesian population. SARS-CoV-2 derived T-cell epitopes were predicted using immunoinformatics tools and assessed for their conservancy, variability, and population coverage. Two fully conserved epitopes with 100% similarity and nine heterologous epitopes with identical T-cell receptor (TCR) contact residues were identified from the ORF1ab fragment of SARS-CoV-2 and all HCCCs. Cross-reactive epitopes from various proteins of SARS-CoV-2 and LAVs were also identified (15 epitopes from BCG, 7 epitopes from MMR, but none from OPV). A majority of the identified epitopes were observed to belong to ORF1ab, further suggesting the vital role of ORF1ab in the coronaviruses family and suggesting it as a candidate for a potential universal coronavirus vaccine that protects against severe disease by inducing cell mediated immunity.
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Affiliation(s)
- Marsia Gustiananda
- Department of Biomedicine, School of Life Sciences, Indonesia International Institute for Life Sciences, Jl. Pulomas Barat Kav 88, Jakarta 13210, Indonesia
- Correspondence:
| | - Vivi Julietta
- Department of Biomedicine, School of Life Sciences, Indonesia International Institute for Life Sciences, Jl. Pulomas Barat Kav 88, Jakarta 13210, Indonesia
| | - Angelika Hermawan
- Department of Biomedicine, School of Life Sciences, Indonesia International Institute for Life Sciences, Jl. Pulomas Barat Kav 88, Jakarta 13210, Indonesia
| | - Gabriella Gita Febriana
- Department of Biomedicine, School of Life Sciences, Indonesia International Institute for Life Sciences, Jl. Pulomas Barat Kav 88, Jakarta 13210, Indonesia
| | - Rio Hermantara
- Department of Biomedicine, School of Life Sciences, Indonesia International Institute for Life Sciences, Jl. Pulomas Barat Kav 88, Jakarta 13210, Indonesia
| | - Lidya Kristiani
- Department of Biomedicine, School of Life Sciences, Indonesia International Institute for Life Sciences, Jl. Pulomas Barat Kav 88, Jakarta 13210, Indonesia
| | - Elizabeth Sidhartha
- Department of Biomedicine, School of Life Sciences, Indonesia International Institute for Life Sciences, Jl. Pulomas Barat Kav 88, Jakarta 13210, Indonesia
| | - Richard Sutejo
- Department of Biomedicine, School of Life Sciences, Indonesia International Institute for Life Sciences, Jl. Pulomas Barat Kav 88, Jakarta 13210, Indonesia
| | - David Agustriawan
- Department of Bioinformatics, School of Life Sciences, Indonesia International Institute for Life Sciences, Jl. Pulomas Barat Kav 88, Jakarta 13210, Indonesia
| | - Sita Andarini
- Department of Pulmonology and Respiratory Medicine, Faculty of Medicine University of Indonesia, Persahabatan Hospital, Jl. Persahabatan Raya 1, Jakarta 13230, Indonesia
| | - Arli Aditya Parikesit
- Department of Bioinformatics, School of Life Sciences, Indonesia International Institute for Life Sciences, Jl. Pulomas Barat Kav 88, Jakarta 13210, Indonesia
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Augusto DG, Yusufali T, Sabatino JJ, Peyser ND, Murdolo LD, Butcher X, Murray V, Pae V, Sarvadhavabhatla S, Beltran F, Gill G, Lynch K, Yun C, Maguire C, Peluso MJ, Hoh R, Henrich TJ, Deeks SG, Davidson M, Lu S, Goldberg SA, Kelly JD, Martin JN, Viera-Green CA, Spellman SR, Langton DJ, Lee S, Marcus GM, Olgin JE, Pletcher MJ, Gras S, Maiers M, Hollenbach JA. A common allele of HLA mediates asymptomatic SARS-CoV-2 infection. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2021.05.13.21257065. [PMID: 34031661 PMCID: PMC8142661 DOI: 10.1101/2021.05.13.21257065] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Despite some inconsistent reporting of symptoms, studies have demonstrated that at least 20% of individuals infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) will remain asymptomatic. Although most global efforts have focused on understanding factors underlying severe illness in COVID-19 (coronavirus disease of 2019), the examination of asymptomatic infection provides a unique opportunity to consider early disease and immunologic features promoting rapid viral clearance. Owing to its critical role in the immune response, we postulated that variation in the human leukocyte antigen (HLA) loci may underly processes mediating asymptomatic infection. We enrolled 29,947 individuals registered in the National Marrow Donor Program for whom high-resolution HLA genotyping data were available in the UCSF Citizen Science smartphone-based study designed to track COVID-19 symptoms and outcomes. Our discovery cohort (n=1428) was comprised of unvaccinated, self-identified subjects who reported a positive test result for SARS-CoV-2. We tested for association of five HLA loci (HLA-A, -B, -C, -DRB1, -DQB1) with disease course and identified a strong association of HLA-B*15:01 with asymptomatic infection, and reproduced this association in two independent cohorts. Suggesting that this genetic association is due to pre-existing T-cell immunity, we show that T cells from pre-pandemic individuals carrying HLA-B*15:01 were reactive to the immunodominant SARS-CoV-2 S-derived peptide NQKLIANQF, and 100% of the reactive cells displayed memory phenotype. Finally, we characterize the protein structure of HLA-B*15:01-peptide complexes, demonstrating that the NQKLIANQF peptide from SARS-CoV-2, and the highly homologous NQKLIANAF from seasonal coronaviruses OC43-CoV and HKU1-CoV, share similar ability to be stabilized and presented by HLA-B*15:01, providing the molecular basis for T-cell cross-reactivity and HLA-B*15:01-mediated pre-existing immunity.
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Affiliation(s)
- Danillo G. Augusto
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, USA
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Curitiba, Brazil
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Tasneem Yusufali
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Joseph J. Sabatino
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Noah D. Peyser
- Division of Cardiology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Lawton D. Murdolo
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Xochitl Butcher
- Division of Cardiology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Victoria Murray
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Vivian Pae
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Sannidhi Sarvadhavabhatla
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Fiona Beltran
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Gurjot Gill
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Kara Lynch
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Cassandra Yun
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Colin Maguire
- University of Utah, Clinical and Translational Science Institute, Salt Lake City, UT
| | - Michael J. Peluso
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Rebecca Hoh
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Timothy J. Henrich
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Steven G. Deeks
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Michelle Davidson
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Scott Lu
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Sarah A. Goldberg
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - J. Daniel Kelly
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
- F.I. Proctor Foundation, University of California San Francisco, San Francisco, CA, USA
| | - Jeffrey N. Martin
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Cynthia A. Viera-Green
- CIBMTR (Center for International Blood and Marrow Transplant Research), National Marrow Donor Program/Be The Match, Minneapolis, Minnesota
| | - Stephen R. Spellman
- CIBMTR (Center for International Blood and Marrow Transplant Research), National Marrow Donor Program/Be The Match, Minneapolis, Minnesota
| | - David J. Langton
- ExplantLab, The Biosphere, Newcastle Helix, Newcastle-upon-Tyne, UK
| | - Sulggi Lee
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Gregory M. Marcus
- Division of Cardiology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Jeffrey E. Olgin
- Division of Cardiology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Mark J. Pletcher
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
- Division of General Internal Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Stephanie Gras
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | | | - Jill A. Hollenbach
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
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Palatnik-de-Sousa I, Wallace ZS, Cavalcante SC, Ribeiro MPF, Silva JABM, Cavalcante RC, Scheuermann RH, Palatnik-de-Sousa CB. A novel vaccine based on SARS-CoV-2 CD4 + and CD8 + T cell conserved epitopes from variants Alpha to Omicron. Sci Rep 2022; 12:16731. [PMID: 36202985 PMCID: PMC9537284 DOI: 10.1038/s41598-022-21207-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 09/23/2022] [Indexed: 12/03/2022] Open
Abstract
COVID-19 caused, as of September, 1rst, 2022, 599,825,400 confirmed cases, including 6,469,458 deaths. Currently used vaccines reduced severity and mortality but not virus transmission or reinfection by different strains. They are based on the Spike protein of the Wuhan reference virus, which although highly antigenic suffered many mutations in SARS-CoV-2 variants, escaping vaccine-generated immune responses. Multiepitope vaccines based on 100% conserved epitopes of multiple proteins of all SARS-CoV-2 variants, rather than a single highly mutating antigen, could offer more long-lasting protection. In this study, a multiepitope multivariant vaccine was designed using immunoinformatics and in silico approaches. It is composed of highly promiscuous and strong HLA binding CD4+ and CD8+ T cell epitopes of the S, M, N, E, ORF1ab, ORF 6 and ORF8 proteins. Based on the analysis of one genome per WHO clade, the epitopes were 100% conserved among the Wuhan-Hu1, Alpha, Beta, Gamma, Delta, Omicron, Mµ, Zeta, Lambda and R1 variants. An extended epitope-conservancy analysis performed using GISAID metadata of 3,630,666 SARS-CoV-2 genomes of these variants and the additional genomes of the Epsilon, Lota, Theta, Eta, Kappa and GH490 R clades, confirmed the high conservancy of the epitopes. All but one of the CD4 peptides showed a level of conservation greater than 97% among all genomes. All but one of the CD8 epitopes showed a level of conservation greater than 96% among all genomes, with the vast majority greater than 99%. A multiepitope and multivariant recombinant vaccine was designed and it was stable, mildly hydrophobic and non-toxic. The vaccine has good molecular docking with TLR4 and promoted, without adjuvant, strong B and Th1 memory immune responses and secretion of high levels of IL-2, IFN-γ, lower levels of IL-12, TGF-β and IL-10, and no IL-6. Experimental in vivo studies should validate the vaccine’s further use as preventive tool with cross-protective properties.
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Affiliation(s)
- Iam Palatnik-de-Sousa
- Department of Electrical Engeneering, Pontifical Catholic University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Zachary S Wallace
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA, USA.,Department of Computer Science and Engineering, University of California, San Diego, CA, USA
| | - Stephany Christiny Cavalcante
- Department of General Microbiology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Maria Paula Fonseca Ribeiro
- Department of General Microbiology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - João Antônio Barbosa Martins Silva
- Department of General Microbiology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Rafael Ciro Cavalcante
- Department of Pharmacy, Campus Professor Antônio Garcia Filho, Federal University of Sergipe, Lagarto, Sergipe, Brazil
| | - Richard H Scheuermann
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA, USA.,Department of Pathology, University of California, San Diego, CA, USA.,Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, USA.,Global Virus Network, Baltimore, MD, USA
| | - Clarisa Beatriz Palatnik-de-Sousa
- Department of General Microbiology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil. .,Institute for Immunological Investigation (III), INCT, National Council for Scientific and Technological Development (CNPq), São Paulo, Brazil.
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47
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Margaroli C, Benson P, Gastanadui MG, Song C, Viera L, Xing D, Wells JM, Patel R, Gaggar A, Payne GA. Spatial transcriptomic profiling of coronary endothelial cells in SARS-CoV-2 myocarditis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.09.25.509426. [PMID: 36203548 PMCID: PMC9536040 DOI: 10.1101/2022.09.25.509426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
OBJECTIVES Our objective was to examine coronary endothelial and myocardial programming in patients with severe COVID-19 utilizing digital spatial transcriptomics. BACKGROUND Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has well-established links to thrombotic and cardiovascular events. Endothelial cell infection was initially proposed to initiate vascular events; however, this paradigm has sparked growing controversy. The significance of myocardial infection also remains unclear. METHODS Autopsy-derived cardiac tissue from control (n = 4) and COVID-19 (n = 8) patients underwent spatial transcriptomic profiling to assess differential expression patterns in myocardial and coronary vascular tissue. Our approach enabled transcriptional profiling in situ with preserved anatomy and unaltered local SARS-CoV-2 expression. In so doing, we examined the paracrine effect of SARS-CoV-2 infection in cardiac tissue. RESULTS We observed heterogeneous myocardial infection that tended to colocalize with CD31 positive cells within coronary capillaries. Despite these differences, COVID-19 patients displayed a uniform and unique myocardial transcriptional profile independent of local viral burden. Segmentation of tissues directly infected with SARS-CoV-2 showed unique, pro-inflammatory expression profiles including upregulated mediators of viral antigen presentation and immune regulation. Infected cell types appeared to primarily be capillary endothelial cells as differentially expressed genes included endothelial cell markers. However, there was limited differential expression within the endothelium of larger coronary vessels. CONCLUSIONS Our results highlight altered myocardial programming during severe COVID-19 that may in part be associated with capillary endothelial cells. However, similar patterns were not observed in larger vessels, diminishing endotheliitis and endothelial activation as key drivers of cardiovascular events during COVID-19. CONDENSED ABSTRACT SARS-CoV-2 is linked to thrombotic and cardiovascular events; however, the mechanism remains uncertain. Our objective was to examine coronary endothelial and myocardial programming in patients with severe COVID-19 utilizing digital spatial transcriptomics. Autopsy-derived coronary arterial and cardiac tissues from control and COVID-19 patients underwent spatial transcriptomic profiling. Our approach enabled transcriptional profiling in situ with preserved anatomy and unaltered local SARS-CoV-2 expression. We observed unique, pro-inflammatory expression profiles among all COVID-19 patients. While heterogeneous viral expression was noted within the tissue, SARS-CoV-2 tended to colocalize with CD31 positive cells within coronary capillaries and was associated with unique expression profiles. Similar patterns were not observed in larger coronary vessels. Our results highlight altered myocardial programming during severe COVID-19 that may in part be associated with capillary endothelial cells. Such results diminish coronary arterial endotheliitis and endothelial activation as key drivers of cardiovascular events during COVID-19 infection. LIST OF HIGHLIGHTS SARS-CoV-2 has variable expression patterns within the myocardium of COVID-19 patientsSARS-CoV-2 infection induces a unique myocardial transcriptional programming independent of local viral burdenSARS-CoV-2 myocarditis is predominantly associated with capillaritis, and tissues directly infected with SARS-CoV-2 have unique, pro-inflammatory expression profilesDiffuse endothelial activation of larger coronary vessels was absent, diminishing large artery endotheliitis as a significant contributor to cardiovascular events during COVID-19 infection.
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Upadhyai P, Shenoy PU, Banjan B, Albeshr MF, Mahboob S, Manzoor I, Das R. Exome-Wide Association Study Reveals Host Genetic Variants Likely Associated with the Severity of COVID-19 in Patients of European Ancestry. Life (Basel) 2022; 12:1300. [PMID: 36143338 PMCID: PMC9504138 DOI: 10.3390/life12091300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 12/03/2022] Open
Abstract
Host genetic variability plays a pivotal role in modulating COVID-19 clinical outcomes. Despite the functional relevance of protein-coding regions, rare variants located here are less likely to completely explain the considerable numbers of acutely affected COVID-19 patients worldwide. Using an exome-wide association approach, with individuals of European descent, we sought to identify common coding variants linked with variation in COVID-19 severity. Herein, cohort 1 compared non-hospitalized (controls) and hospitalized (cases) individuals, and in cohort 2, hospitalized subjects requiring respiratory support (cases) were compared to those not requiring it (controls). 229 and 111 variants differed significantly between cases and controls in cohorts 1 and 2, respectively. This included FBXO34, CNTN2, and TMCC2 previously linked with COVID-19 severity using association studies. Overall, we report SNPs in 26 known and 12 novel candidate genes with strong molecular evidence implicating them in the pathophysiology of life-threatening COVID-19 and post-recovery sequelae. Of these few notable known genes include, HLA-DQB1, AHSG, ALOX5AP, MUC5AC, SMPD1, SPG7, SPEG,GAS6, and SERPINA12. These results enhance our understanding of the pathomechanisms underlying the COVID-19 clinical spectrum and may be exploited to prioritize biomarkers for predicting disease severity, as well as to improve treatment strategies in individuals of European ancestry.
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Affiliation(s)
- Priyanka Upadhyai
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal 576104, India
| | - Pooja U. Shenoy
- Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
| | - Bhavya Banjan
- Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, India
| | - Mohammed F. Albeshr
- Department of Zoology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Shahid Mahboob
- Department of Zoology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Irfan Manzoor
- Department of Biology, The College of Arts and Sciences, Indiana University, Bloomington, IN 47405, USA
| | - Ranajit Das
- Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
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Khare K, Pandey R. Cellular heterogeneity in disease severity and clinical outcome: Granular understanding of immune response is key. Front Immunol 2022; 13:973070. [PMID: 36072602 PMCID: PMC9441806 DOI: 10.3389/fimmu.2022.973070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 07/26/2022] [Indexed: 12/15/2022] Open
Abstract
During an infectious disease progression, it is crucial to understand the cellular heterogeneity underlying the differential immune response landscape that will augment the precise information of the disease severity modulators, leading to differential clinical outcome. Patients with COVID-19 display a complex yet regulated immune profile with a heterogeneous array of clinical manifestation that delineates disease severity sub-phenotypes and worst clinical outcomes. Therefore, it is necessary to elucidate/understand/enumerate the role of cellular heterogeneity during COVID-19 disease to understand the underlying immunological mechanisms regulating the disease severity. This article aims to comprehend the current findings regarding dysregulation and impairment of immune response in COVID-19 disease severity sub-phenotypes and relate them to a wide array of heterogeneous populations of immune cells. On the basis of the findings, it suggests a possible functional correlation between cellular heterogeneity and the COVID-19 disease severity. It highlights the plausible modulators of age, gender, comorbidities, and hosts' genetics that may be considered relevant in regulating the host response and subsequently the COVID-19 disease severity. Finally, it aims to highlight challenges in COVID-19 disease that can be achieved by the application of single-cell genomics, which may aid in delineating the heterogeneity with more granular understanding. This will augment our future pandemic preparedness with possibility to identify the subset of patients with increased diseased severity.
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Affiliation(s)
- Kriti Khare
- Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Rajesh Pandey
- Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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Dobrijević Z, Gligorijević N, Šunderić M, Penezić A, Miljuš G, Tomić S, Nedić O. The association of human leucocyte antigen (HLA) alleles with COVID-19 severity: A systematic review and meta-analysis. Rev Med Virol 2022; 33:e2378. [PMID: 35818892 PMCID: PMC9349710 DOI: 10.1002/rmv.2378] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 05/10/2022] [Accepted: 07/04/2022] [Indexed: 01/28/2023]
Abstract
Due to their pivotal role in orchestrating the immune response, HLA loci were recognized as candidates for genetic association studies related to the severity of COVID-19. Since the findings on the effects of HLA alleles on the outcome of SARS-CoV-2 infection remain inconclusive, we aimed to elucidate the potential involvement of genetic variability within HLA loci in the molecular genetics of COVID-19 by classifying the articles according to different disease severity/outcomes and by conducting a systematic review with meta-analysis. Potentially eligible studies were identified by searching PubMed, Scopus and Web of Science literature databases. A total of 28 studies with 13,073 participants were included in qualitative synthesis, while the results of 19 studies with 10,551 SARS-CoV-2-positive participants were pooled in the meta-analysis. According to the results of quantitative data synthesis, association with COVID-19 severity or with the lethal outcome was determined for the following alleles and allele families: HLA-A*01, HLA-A*03, HLA-A*11, HLA-A*23, HLA-A*31, HLA-A*68, HLA-A*68:02, HLA-B*07:02, HLA-B*14, HLA-B*15, HLA-B*40:02, HLA-B*51:01, HLA-B*53, HLA-B*54, HLA-B*54:01, HLA-C*04, HLA-C*04:01, HLA-C*06, HLA-C*07:02, HLA-DRB1*11, HLA-DRB1*15, HLA-DQB1*03 and HLA-DQB1*06 (assuming either allelic or dominant genetic model). We conclude that alleles of HLA-A, -B, -C, -DRB1 and -DQB1 loci may represent potential biomarkers of COVID-19 severity and/or mortality, which needs to be confirmed in a larger set of studies.
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Affiliation(s)
- Zorana Dobrijević
- Department for MetabolismUniversity of Belgrade—Institute for the Application of Nuclear EnergyBelgradeSerbia
| | - Nikola Gligorijević
- Department for MetabolismUniversity of Belgrade—Institute for the Application of Nuclear EnergyBelgradeSerbia
| | - Miloš Šunderić
- Department for MetabolismUniversity of Belgrade—Institute for the Application of Nuclear EnergyBelgradeSerbia
| | - Ana Penezić
- Department for MetabolismUniversity of Belgrade—Institute for the Application of Nuclear EnergyBelgradeSerbia
| | - Goran Miljuš
- Department for MetabolismUniversity of Belgrade—Institute for the Application of Nuclear EnergyBelgradeSerbia
| | - Sergej Tomić
- Department for Immunology and ImmunoparasitologyUniversity of Belgrade—Institute for the Application of Nuclear EnergyBelgradeSerbia
| | - Olgica Nedić
- Department for MetabolismUniversity of Belgrade—Institute for the Application of Nuclear EnergyBelgradeSerbia
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